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- PDB-3vx3: Crystal structure of [NiFe] hydrogenase maturation protein HypB f... -

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Basic information

Entry
Database: PDB / ID: 3vx3
TitleCrystal structure of [NiFe] hydrogenase maturation protein HypB from Thermococcus kodakarensis KOD1
ComponentsATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
KeywordsADP BINDING PROTEIN / Mrp/MinD family ATPase / [NiFe] hydrogenase maturation
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
ADENOSINE-5'-DIPHOSPHATE / Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSasaki, D. / Watanabe, S. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation
Authors: Sasaki, D. / Watanabe, S. / Matsumi, R. / Shoji, T. / Yasukochi, A. / Tagashira, K. / Fukuda, W. / Kanai, T. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionSep 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,47110
Polymers55,2442
Non-polymers1,2278
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-13 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.241, 137.689, 150.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 27622.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2007 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q5JIH4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 40492 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rsym value: 0.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.529 / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→40.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.403 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21845 2010 5 %RANDOM
Rwork0.19362 ---
obs0.19485 38324 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.133 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2--0.22 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 78 175 3931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223816
X-RAY DIFFRACTIONr_angle_refined_deg1.4972.0315154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25123.867150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83815696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9331526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212738
X-RAY DIFFRACTIONr_mcbond_it0.6991.52326
X-RAY DIFFRACTIONr_mcangle_it1.28623766
X-RAY DIFFRACTIONr_scbond_it2.10131490
X-RAY DIFFRACTIONr_scangle_it3.4494.51388
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 159 -
Rwork0.268 2766 -
obs--99.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.07220.29190.0592.90191.02932.53210.01860.0196-0.07910.11070.1-0.2780.03270.0716-0.11860.06690.0245-0.01160.1182-0.10180.1068-14.8587-13.7326-17.6177
22.8297-0.4087-0.14042.32030.93011.162-0.04740.0951-0.1338-0.0510.00660.09570.0839-0.03170.04080.07230.001-0.02050.0986-0.10860.1285-40.4321-23.3619-27.5738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 248
2X-RAY DIFFRACTION2B4 - 248

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