3TJ7 | pdb_00003tj7

GBAA_1210 protein, a putative adenylate cyclase, from Bacillus anthracis in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb3TJ7/pdb

Classification: LYASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-08-23 Released: 2011-08-31
Deposition Author(s): Osipiuk, J., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

GBAA_1210 protein, a putative adenylate cyclase, from Bacillus anthracis in complex with AMP

Osipiuk, J., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 92.9 kDa
Atom Count: 6,154
Modeled Residue Count: 705
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GBAA_1210 protein	A, B, C, D	195	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 1 Gene Names: BAS1117, BA_1210, GBAA_1210
UniProt
Find proteins for A0A6L8P3N5 (Bacillus anthracis) Explore A0A6L8P3N5 Go to UniProtKB: A0A6L8P3N5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8P3N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], J [auth C], O [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain F [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain F [auth A]	F [auth A], P [auth D], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain P [auth D] Focus chain Q [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth C] L [auth C] M [auth C] G [auth A], H [auth A], K [auth C], L [auth C], M [auth C], N [auth C], R [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.245 (Depositor), 0.240 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33tj7

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.229	α = 90
b = 86.315	β = 102.02
c = 76.438	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-11-27
Changes: Structure summary