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- PDB-5aun: Crystal structure of the HypAB-Ni complex -

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Basic information

Entry
Database: PDB / ID: 5aun
TitleCrystal structure of the HypAB-Ni 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
ADENOSINE-5'-DIPHOSPHATE / NICKEL (II) ION / UREA / Hydrogenase maturation factor HypA / Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesThermococcus kodakaraensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,33413
Polymers43,3342
Non-polymers1,00011
Water6,287349
1
A: Probable hydrogenase nickel incorporation protein HypA
B: ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)88,66726
Polymers86,6684
Non-polymers1,99922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14500 Å2
ΔGint-131 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.720, 82.744, 65.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-537-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Probable hydrogenase nickel incorporation protein HypA


Mass: 15711.977 Da / Num. of mol.: 1
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.: 1
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 , 8 types, 360 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: CH4N2O
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2 / Details: Magnesium chloride, PEG3350

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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: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 101768 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.81 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.038 / Rrim(I) all: 0.09 / Χ2: 0.978 / Net I/av σ(I): 19.243 / Net I/σ(I): 6.1 / Num. measured all: 316919
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.63-1.664.524230.5040.5310.74997.5
1.66-1.694.824850.6270.4920.75899.2
1.69-1.725.525230.6920.4380.7621000.957
1.72-1.766.425090.8240.3460.7361000.8160.888
1.76-1.796.625120.8570.2960.7781000.7120.772
1.79-1.846.725320.8810.2470.7861000.5930.644
1.84-1.886.725020.9190.2080.8211000.4990.541
1.88-1.936.625280.9440.1630.8281000.390.424
1.93-1.996.525260.9650.1260.8751000.2990.325
1.99-2.056.425180.9730.1070.9161000.2510.273
2.05-2.136.125260.9790.0890.9741000.2020.221
2.13-2.215.925470.9850.0711.0541000.1580.173
2.21-2.316.325560.9870.0621.1391000.1440.157
2.31-2.436.225380.9890.0531.1911000.1220.133
2.43-2.596.825610.9930.0431.2441000.1040.113
2.59-2.796.825470.9930.0381.2811000.0910.099
2.79-3.076.725760.9940.0331.2831000.0780.085
3.07-3.516.425850.9960.0271.191000.0630.069
3.51-4.42626260.9970.0221.0311000.0510.055
4.42-506.527640.9970.0210.93999.90.050.054

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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: 1.63→37.36 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 23.51 / Stereochemistry target values: ML
Details: THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2131 4910 5.07 %
Rwork0.1804 91978 -
obs0.1821 96888 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.99 Å2 / Biso mean: 29.8632 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: final / Resolution: 1.63→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 56 349 3323
Biso mean--36.68 39.46 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073105
X-RAY DIFFRACTIONf_angle_d0.9074184
X-RAY DIFFRACTIONf_chiral_restr0.034477
X-RAY DIFFRACTIONf_plane_restr0.004539
X-RAY DIFFRACTIONf_dihedral_angle_d14.3121147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6298-1.64840.34261540.30562682283688
1.6484-1.66780.32011770.31482994317198
1.6678-1.68810.34671720.29763045321799
1.6881-1.70950.32181550.287831183273100
1.7095-1.7320.30491720.264930623234100
1.732-1.75570.29591570.265630923249100
1.7557-1.78080.32861580.262930473205100
1.7808-1.80730.27281810.255230953276100
1.8073-1.83560.33861640.24230963260100
1.8356-1.86570.27731460.238831183264100
1.8657-1.89790.2211770.219630363213100
1.8979-1.93240.28091730.209530593232100
1.9324-1.96950.23281730.198930883261100
1.9695-2.00970.23391560.193931063262100
2.0097-2.05340.22591550.189330683223100
2.0534-2.10120.24031740.194830963270100
2.1012-2.15370.24271610.188530763237100
2.1537-2.2120.25551590.182130673226100
2.212-2.2770.2211720.183330883260100
2.277-2.35050.20631740.173730773251100
2.3505-2.43450.18291510.174231043255100
2.4345-2.5320.19781480.174130903238100
2.532-2.64720.19331940.176830513245100
2.6472-2.78670.24191720.177630683240100
2.7867-2.96120.19651500.181531033253100
2.9612-3.18970.21561530.175730943247100
3.1897-3.51050.17261490.161131003249100
3.5105-4.0180.16671720.143330663238100
4.018-5.06030.1391640.134430863250100
5.0603-37.36980.23451470.175431063253100

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