4GF5

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
R-Value Work: 0.159
R-Value Observed: 0.159

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
Modelled Residue Count: 5,020
Deposited Residue Count: 5,140
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 DB [auth O] SDF format, chain BA [auth F] SDF format, chain BB [auth N] 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 JB [auth R] SDF format, chain KA [auth G] SDF format, chain LB [auth S] SDF format, chain NA [auth I] SDF format, chain OB [auth T] SDF format, chain PA [auth J] SDF format, chain SA [auth K] SDF format, chain U [auth A] SDF format, chain VA [auth L] SDF format, chain W [auth C] SDF format, chain Y [auth E] SDF format, chain YA [auth M] MOL2 format, chain DB [auth O] MOL2 format, chain BA [auth F] MOL2 format, chain BB [auth N] 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 JB [auth R] MOL2 format, chain KA [auth G] MOL2 format, chain LB [auth S] MOL2 format, chain NA [auth I] MOL2 format, chain OB [auth T] MOL2 format, chain PA [auth J] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain YA [auth M]	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 FA [auth H] SDF format, chain LA [auth G] 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 GB [auth P] SDF format, chain HA [auth B] SDF format, chain IB [auth Q] SDF format, chain JA [auth D] SDF format, chain KB [auth R] SDF format, chain MA [auth G] SDF format, chain MB [auth S] SDF format, chain NB [auth S] SDF format, chain OA [auth I] 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] MOL2 format, chain FA [auth H] MOL2 format, chain LA [auth G] 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 GB [auth P] MOL2 format, chain HA [auth B] MOL2 format, chain IB [auth Q] MOL2 format, chain JA [auth D] MOL2 format, chain KB [auth R] MOL2 format, chain MA [auth G] MOL2 format, chain MB [auth S] MOL2 format, chain NB [auth S] MOL2 format, chain OA [auth I] 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]	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
R-Value Work: 0.159
R-Value Observed: 0.159
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

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