3NGW | pdb_00003ngw

Crystal Structure of Molybdopterin-guanine dinucleotide biosynthesis protein A from Archaeoglobus fulgidus, Northeast Structural Genomics Consortium Target GR189

PDB DOI: https://doi.org/10.2210/pdb3NGW/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-06-13 Released: 2010-08-11
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.226 (Depositor), 0.236 (DCC)
R-Value Work:
0.183 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target GR189

Forouhar, F., Neely, H., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 24.1 kDa
Atom Count: 1,619
Modeled Residue Count: 195
Deposited Residue Count: 208
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin-guanine dinucleotide biosynthesis protein A (MobA)	A	208	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: AF_2005, mobA
UniProt
Find proteins for O28274 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28274 Go to UniProtKB: O28274
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O28274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.226 (Depositor), 0.236 (DCC)
R-Value Work: 0.183 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.1	α = 90
b = 116.1	β = 90
c = 116.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-08-11

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary