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- PDB-2wsm: Crystal structure of Hydrogenase Maturation Factor HypB From Arch... -

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Basic information

Entry
Database: PDB / ID: 2wsm
TitleCrystal structure of Hydrogenase Maturation Factor HypB From Archaeoglobus Fulgidus
ComponentsHYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPB)
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


nickel cation binding / protein maturation / GTPase activity / zinc ion binding
Similarity search - Function
Hydrogenase maturation factor HypB / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase expression/formation protein (HypB)
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWong, K.B. / Li, T.
CitationJournal: Plos One / Year: 2012
Title: Structural Basis for GTP-Dependent Dimerization of Hydrogenase Maturation Factor Hypb.
Authors: Chan, K.H. / Li, T. / Wong, C. / Wong, K.B.
History
DepositionSep 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR
Remark 700 SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPB)
B: HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4283
Polymers49,3932
Non-polymers351
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-20.8 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.494, 82.325, 68.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPB)


Mass: 24696.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: DSM 4304 / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O28903
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.82 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→42.76 Å / Num. obs: 18861 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 20 % / Biso Wilson estimate: 36.08 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HF8

2hf8


Resolution: 2.3→42.64 Å / SU ML: 1.86 / σ(F): 0.02 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 960 5.1 %
Rwork0.223 --
obs0.226 18704 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.84 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 41.24 Å2
Baniso -1Baniso -2Baniso -3
1-9.7536 Å20 Å20 Å2
2---3.7824 Å20 Å2
3----5.9711 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 1 138 3157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053051
X-RAY DIFFRACTIONf_angle_d0.8294096
X-RAY DIFFRACTIONf_dihedral_angle_d15.9651159
X-RAY DIFFRACTIONf_chiral_restr0.057479
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2992-2.42040.31381360.22972383X-RAY DIFFRACTION95
2.4204-2.5720.28591430.21782492X-RAY DIFFRACTION99
2.572-2.77060.29191250.21832523X-RAY DIFFRACTION100
2.7706-3.04930.31471210.22192551X-RAY DIFFRACTION100
3.0493-3.49040.27781340.22442537X-RAY DIFFRACTION100
3.4904-4.39680.2541410.20752574X-RAY DIFFRACTION100
4.3968-42.64850.25841600.22722684X-RAY DIFFRACTION100

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