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- PDB-5aup: Crystal structure of the HypAB complex -

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Basic information

Entry
Database: PDB / ID: 5aup
TitleCrystal structure of the HypAB complex
Components
  • ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
  • Probable hydrogenase nickel incorporation protein HypA
KeywordsMETAL BINDING PROTEIN/HYDROLASE / protein complex / metallochaperone / METAL BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / nickel cation binding / protein maturation / protein modification process / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / zinc ion binding / ATP binding / metal ion binding
Similarity search - Function
hypothetical protein PF0899 fold - #50 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Iron-sulfur protein NUBPL-like / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / hypothetical protein PF0899 fold ...hypothetical protein PF0899 fold - #50 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Iron-sulfur protein NUBPL-like / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / hypothetical protein PF0899 fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Hydrogenase maturation factor HypA / Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesThermococcus kodakaraensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 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 / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable hydrogenase nickel incorporation protein HypA
B: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
H: Probable hydrogenase nickel incorporation protein HypA
I: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,85810
Polymers86,6684
Non-polymers1,1906
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-91 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.945, 123.931, 55.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules AHBI

#1: Protein Probable hydrogenase nickel incorporation protein HypA


Mass: 15711.977 Da / Num. of mol.: 2
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: hypA, TK2008 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIH3
#2: Protein ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog / HypB


Mass: 27622.047 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 13 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
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: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 31382 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.4

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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: 3A43 and 3VX3

3a43

3vx3


Resolution: 3.102→46.537 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 25.96 / Stereochemistry target values: ML
Details: THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2385 1458 5.02 %
Rwork0.1947 --
obs0.1969 29043 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.102→46.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 0 66 7 5850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035969
X-RAY DIFFRACTIONf_angle_d0.5278077
X-RAY DIFFRACTIONf_dihedral_angle_d12.3712155
X-RAY DIFFRACTIONf_chiral_restr0.02938
X-RAY DIFFRACTIONf_plane_restr0.0031026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1017-3.21250.37931270.31972664X-RAY DIFFRACTION96
3.2125-3.34110.37321540.29772736X-RAY DIFFRACTION100
3.3411-3.49310.2881490.25252779X-RAY DIFFRACTION100
3.4931-3.67720.30041510.22962801X-RAY DIFFRACTION100
3.6772-3.90750.24811330.20842746X-RAY DIFFRACTION100
3.9075-4.2090.21521450.18292796X-RAY DIFFRACTION100
4.209-4.63220.21661550.15872749X-RAY DIFFRACTION100
4.6322-5.30170.20011490.16512769X-RAY DIFFRACTION100
5.3017-6.67650.27011400.1972791X-RAY DIFFRACTION100
6.6765-46.54220.18071550.15532754X-RAY DIFFRACTION100

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