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- PDB-5auq: Crystal structure of ATPase-type HypB in the nucleotide free state -

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Basic information

Entry
Database: PDB / ID: 5auq
TitleCrystal structure of ATPase-type HypB in the nucleotide free state
ComponentsATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
KeywordsHYDROLASE / ATPase
Function / homology
Function and homology information


ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Iron-sulfur protein NUBPL-like / Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesThermococcus kodakaraensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.525 Å
AuthorsWatanabe, S. / Kawashima, T. / Nishitani, Y. / Miki, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer
Authors: Watanabe, S. / Kawashima, T. / Nishitani, Y. / Kanai, T. / Wada, T. / Inaba, K. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionMay 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: cell / citation ...cell / citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _cell.Z_PDB / _citation.journal_id_CSD ..._cell.Z_PDB / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
B: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
C: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
D: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
E: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
F: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
G: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
H: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,16110
Polymers220,9768
Non-polymers1842
Water3,657203
1
A: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
H: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3363
Polymers55,2442
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-7 kcal/mol
Surface area18250 Å2
MethodPISA
2
B: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
E: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3363
Polymers55,2442
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area17490 Å2
MethodPISA
3
C: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
G: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog


Theoretical massNumber of molelcules
Total (without water)55,2442
Polymers55,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-4 kcal/mol
Surface area18460 Å2
MethodPISA
4
D: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
F: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog


Theoretical massNumber of molelcules
Total (without water)55,2442
Polymers55,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-9 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.294, 77.901, 122.928
Angle α, β, γ (deg.)90.00, 104.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog / HypB


Mass: 27622.047 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIH4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Magnesium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 73757 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.5
Reflection shellResolution: 2.51→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VX3

3vx3


Resolution: 2.525→40.601 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 3712 5.04 %
Rwork0.2143 --
obs0.2159 73651 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.525→40.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13836 0 12 203 14051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214084
X-RAY DIFFRACTIONf_angle_d0.54419093
X-RAY DIFFRACTIONf_dihedral_angle_d11.4675162
X-RAY DIFFRACTIONf_chiral_restr0.0212302
X-RAY DIFFRACTIONf_plane_restr0.0032416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5247-2.55670.37061390.31582326X-RAY DIFFRACTION89
2.5567-2.59030.33781460.30012554X-RAY DIFFRACTION100
2.5903-2.62580.30911440.27512544X-RAY DIFFRACTION100
2.6258-2.66330.31311430.29012596X-RAY DIFFRACTION99
2.6633-2.7030.31211590.27932569X-RAY DIFFRACTION100
2.703-2.74520.35681220.2692594X-RAY DIFFRACTION100
2.7452-2.79020.3491310.27522604X-RAY DIFFRACTION100
2.7902-2.83830.30751260.27432578X-RAY DIFFRACTION100
2.8383-2.88990.30631360.26222587X-RAY DIFFRACTION100
2.8899-2.94550.27441210.2682594X-RAY DIFFRACTION100
2.9455-3.00560.27191420.26172605X-RAY DIFFRACTION100
3.0056-3.0710.32741490.25012569X-RAY DIFFRACTION100
3.071-3.14240.2711290.25362597X-RAY DIFFRACTION100
3.1424-3.22090.28951310.25152628X-RAY DIFFRACTION100
3.2209-3.3080.29261470.24192578X-RAY DIFFRACTION100
3.308-3.40530.251570.22742570X-RAY DIFFRACTION100
3.4053-3.51510.24591420.21632601X-RAY DIFFRACTION100
3.5151-3.64070.26371130.21252621X-RAY DIFFRACTION100
3.6407-3.78630.24221240.19982586X-RAY DIFFRACTION100
3.7863-3.95850.23051590.19532579X-RAY DIFFRACTION100
3.9585-4.1670.24611360.17682606X-RAY DIFFRACTION100
4.167-4.42780.1991480.18352616X-RAY DIFFRACTION100
4.4278-4.76920.18971490.16412625X-RAY DIFFRACTION100
4.7692-5.24820.21251500.17832602X-RAY DIFFRACTION100
5.2482-6.00560.24931390.20812648X-RAY DIFFRACTION100
6.0056-7.55840.23371030.21852672X-RAY DIFFRACTION100
7.5584-40.60640.17951270.18452690X-RAY DIFFRACTION98

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