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- PDB-3a44: Crystal structure of HypA in the dimeric form -

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Basic information

Entry
Database: PDB / ID: 3a44
TitleCrystal structure of HypA in the dimeric form
ComponentsHydrogenase nickel incorporation protein hypA
KeywordsMETAL BINDING PROTEIN / [NiFe] hydrogenase maturation / zinc-finger / nickel binding / domain swapping / Metal-binding / Nickel
Function / homology
Function and homology information


nickel cation binding / protein maturation / protein modification process / zinc ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #120 / hypothetical protein PF0899 fold - #50 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / hypothetical protein PF0899 fold / Rhinovirus 14, subunit 4 / Few Secondary Structures / Irregular ...Rhinovirus 14, subunit 4 - #120 / hypothetical protein PF0899 fold - #50 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / hypothetical protein PF0899 fold / Rhinovirus 14, subunit 4 / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase maturation factor HypA
Similarity search - Component
Biological speciesPyrococcus kodakaraensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsWatanabe, S. / Arai, T. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation.
Authors: Watanabe, S. / Arai, T. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionJun 30, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Dec 11, 2019Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.4Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id / _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: Hydrogenase nickel incorporation protein hypA
B: Hydrogenase nickel incorporation protein hypA
C: Hydrogenase nickel incorporation protein hypA
D: Hydrogenase nickel incorporation protein hypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2228
Polymers62,9604
Non-polymers2624
Water0
1
A: Hydrogenase nickel incorporation protein hypA
B: Hydrogenase nickel incorporation protein hypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6114
Polymers31,4802
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-129 kcal/mol
Surface area16630 Å2
MethodPISA
2
C: Hydrogenase nickel incorporation protein hypA
D: Hydrogenase nickel incorporation protein hypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6114
Polymers31,4802
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-124 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.830, 97.975, 136.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hydrogenase nickel incorporation protein hypA / HypA


Mass: 15739.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus kodakaraensis (archaea) / Strain: KOD1 / Gene: hypA / Plasmid: pET21(+)a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codonplus(DE3)-RIL / References: UniProt: Q5JIH3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 24% PEG8000, 22% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 24, 2008
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 11039 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.092 / Net I/σ(I): 16.7
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 741 / Rsym value: 0.454 / % possible all: 63.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A43

3a43


Resolution: 3.31→49.16 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1639961.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.337 539 4.9 %RANDOM
Rwork0.292 ---
obs0.292 10976 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.3798 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 125 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--46.8 Å20 Å2
3----46.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 3.31→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3848 0 4 0 3852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 58 4.9 %
Rwork0.42 1135 -
obs--61 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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