4GF5 | pdb_00004gf5

Crystal Structure of Calicheamicin Methyltransferase, CalS11

PDB DOI: https://doi.org/10.2210/pdb4GF5/pdb

Classification: TRANSFERASE
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-08-02 Released: 2012-08-22
Deposition Author(s): Helmich, K.E., Singh, S., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.215 (DCC)
R-Value Work:
0.159 (Depositor), 0.161 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

To be published.

Macromolecule Content

Total Structure Weight: 589.39 kDa
Atom Count: 43,522
Modeled Residue Count: 5,020
Deposited Residue Count: 5,140
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalS11	A B [auth C] C [auth E] D [auth F] E [auth H] A, B [auth C], C [auth E], D [auth F], E [auth H], F [auth B], G [auth D], H [auth G], I, J, K, L, M, N, O, P, Q, R, S, T	257	Micromonospora echinospora	Mutation(s): 0 Gene Names: AAM70337, calS11
UniProt
Find proteins for Q8KNF1 (Micromonospora echinospora) Explore Q8KNF1 Go to UniProtKB: Q8KNF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KNF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain BB [auth N] SDF format, chain DB [auth O] SDF format, chain EA [auth H] SDF format, chain FB [auth P] SDF format, chain GA [auth B] SDF format, chain HB [auth Q] SDF format, chain IA [auth D] SDF format, chain KA [auth G] SDF format, chain LB [auth S] SDF format, chain OB [auth T] SDF format, chain PA [auth J] SDF format, chain SA [auth K] SDF format, chain VA [auth L] SDF format, chain W [auth C] SDF format, chain Y [auth E] SDF format, chain YA [auth M] SDF format, chain U [auth A] SDF format, chain NA [auth I] SDF format, chain JB [auth R] MOL2 format, chain BA [auth F] MOL2 format, chain BB [auth N] MOL2 format, chain DB [auth O] MOL2 format, chain EA [auth H] MOL2 format, chain FB [auth P] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth Q] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth G] MOL2 format, chain LB [auth S] MOL2 format, chain OB [auth T] MOL2 format, chain PA [auth J] MOL2 format, chain SA [auth K] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain YA [auth M] MOL2 format, chain U [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain JB [auth R] mmCIF format, chain BA [auth F] mmCIF format, chain BB [auth N] mmCIF format, chain DB [auth O] mmCIF format, chain EA [auth H] mmCIF format, chain FB [auth P] mmCIF format, chain GA [auth B] mmCIF format, chain HB [auth Q] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth G] mmCIF format, chain LB [auth S] mmCIF format, chain OB [auth T] mmCIF format, chain PA [auth J] mmCIF format, chain SA [auth K] mmCIF format, chain VA [auth L] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain YA [auth M] mmCIF format, chain U [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain JB [auth R]	BA [auth F] BB [auth N] DB [auth O] EA [auth H] FB [auth P] BA [auth F], BB [auth N], DB [auth O], EA [auth H], FB [auth P], GA [auth B], HB [auth Q], IA [auth D], JB [auth R], KA [auth G], LB [auth S], NA [auth I], OB [auth T], PA [auth J], SA [auth K], U [auth A], VA [auth L], W [auth C], Y [auth E], YA [auth M]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain BA [auth F] Focus chain BB [auth N] Focus chain DB [auth O] Focus chain EA [auth H] Focus chain FB [auth P] Focus chain GA [auth B] Focus chain HB [auth Q] Focus chain IA [auth D] Focus chain JB [auth R] Focus chain KA [auth G] Focus chain LB [auth S] Focus chain NA [auth I] Focus chain OB [auth T] Focus chain PA [auth J] Focus chain SA [auth K] Focus chain U [auth A] Focus chain VA [auth L] Focus chain W [auth C] Focus chain Y [auth E] Focus chain YA [auth M] Interactions & Density Focus chain BA [auth F] Focus chain BB [auth N] Focus chain DB [auth O] Focus chain EA [auth H] Focus chain FB [auth P] Focus chain GA [auth B] Focus chain HB [auth Q] Focus chain IA [auth D] Focus chain JB [auth R] Focus chain KA [auth G] Focus chain LB [auth S] Focus chain NA [auth I] Focus chain OB [auth T] Focus chain PA [auth J] Focus chain SA [auth K] Focus chain U [auth A] Focus chain VA [auth L] Focus chain W [auth C] Focus chain Y [auth E] Focus chain YA [auth M]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain AB [auth M] SDF format, chain CA [auth F] SDF format, chain CB [auth N] SDF format, chain DA [auth F] SDF format, chain EB [auth O] SDF format, chain FA [auth H] SDF format, chain GB [auth P] SDF format, chain HA [auth B] SDF format, chain IB [auth Q] SDF format, chain KB [auth R] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain MB [auth S] SDF format, chain NB [auth S] SDF format, chain PB [auth T] SDF format, chain QA [auth J] SDF format, chain RA [auth J] SDF format, chain TA [auth K] SDF format, chain UA [auth K] SDF format, chain V [auth A] SDF format, chain WA [auth L] SDF format, chain X [auth C] SDF format, chain XA [auth L] SDF format, chain Z [auth E] SDF format, chain ZA [auth M] SDF format, chain OA [auth I] SDF format, chain JA [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain AB [auth M] MOL2 format, chain CA [auth F] MOL2 format, chain CB [auth N] MOL2 format, chain DA [auth F] MOL2 format, chain EB [auth O] MOL2 format, chain FA [auth H] MOL2 format, chain GB [auth P] MOL2 format, chain HA [auth B] MOL2 format, chain IB [auth Q] MOL2 format, chain KB [auth R] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain MB [auth S] MOL2 format, chain NB [auth S] MOL2 format, chain PB [auth T] MOL2 format, chain QA [auth J] MOL2 format, chain RA [auth J] MOL2 format, chain TA [auth K] MOL2 format, chain UA [auth K] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth L] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth L] MOL2 format, chain Z [auth E] MOL2 format, chain ZA [auth M] MOL2 format, chain OA [auth I] MOL2 format, chain JA [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain AB [auth M] mmCIF format, chain CA [auth F] mmCIF format, chain CB [auth N] mmCIF format, chain DA [auth F] mmCIF format, chain EB [auth O] mmCIF format, chain FA [auth H] mmCIF format, chain GB [auth P] mmCIF format, chain HA [auth B] mmCIF format, chain IB [auth Q] mmCIF format, chain KB [auth R] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain MB [auth S] mmCIF format, chain NB [auth S] mmCIF format, chain PB [auth T] mmCIF format, chain QA [auth J] mmCIF format, chain RA [auth J] mmCIF format, chain TA [auth K] mmCIF format, chain UA [auth K] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth L] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth L] mmCIF format, chain Z [auth E] mmCIF format, chain ZA [auth M] mmCIF format, chain OA [auth I] mmCIF format, chain JA [auth D]	AA [auth E] AB [auth M] CA [auth F] CB [auth N] DA [auth F] AA [auth E], AB [auth M], CA [auth F], CB [auth N], DA [auth F], EB [auth O], FA [auth H], GB [auth P], HA [auth B], IB [auth Q], JA [auth D], KB [auth R], LA [auth G], MA [auth G], MB [auth S], NB [auth S], OA [auth I], PB [auth T], QA [auth J], RA [auth J], TA [auth K], UA [auth K], V [auth A], WA [auth L], X [auth C], XA [auth L], Z [auth E], ZA [auth M]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain AB [auth M] Focus chain CA [auth F] Focus chain CB [auth N] Focus chain DA [auth F] Focus chain EB [auth O] Focus chain FA [auth H] Focus chain GB [auth P] Focus chain HA [auth B] Focus chain IB [auth Q] Focus chain JA [auth D] Focus chain KB [auth R] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain MB [auth S] Focus chain NB [auth S] Focus chain OA [auth I] Focus chain PB [auth T] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain TA [auth K] Focus chain UA [auth K] Focus chain V [auth A] Focus chain WA [auth L] Focus chain X [auth C] Focus chain XA [auth L] Focus chain Z [auth E] Focus chain ZA [auth M] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth M] Focus chain CA [auth F] Focus chain CB [auth N] Focus chain DA [auth F] Focus chain EB [auth O] Focus chain FA [auth H] Focus chain GB [auth P] Focus chain HA [auth B] Focus chain IB [auth Q] Focus chain JA [auth D] Focus chain KB [auth R] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain MB [auth S] Focus chain NB [auth S] Focus chain OA [auth I] Focus chain PB [auth T] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain TA [auth K] Focus chain UA [auth K] Focus chain V [auth A] Focus chain WA [auth L] Focus chain X [auth C] Focus chain XA [auth L] Focus chain Z [auth E] Focus chain ZA [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.213 (Depositor), 0.215 (DCC)
R-Value Work: 0.159 (Depositor), 0.161 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.112	α = 80.88
b = 106.24	β = 81.65
c = 184.6	γ = 70.02

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2012-08-22
Type: Initial release
Version 1.1: 2017-11-15
Changes: Advisory, Refinement description
Version 1.2: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description