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- PDB-3a43: Crystal structure of HypA -

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Basic information

Entry
Database: PDB / ID: 3a43
TitleCrystal structure of HypA
ComponentsHydrogenase nickel incorporation protein hypA
KeywordsMETAL BINDING PROTEIN / [NiFe] hydrogenase maturation / zinc-finger / nickel binding / Metal-binding / Nickel
Function / homology
Function and homology information


nickel cation binding / protein maturation / protein modification process / zinc ion binding
Similarity search - Function
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 / Rubrerythrin, domain 2 - #10 / Rubrerythrin, domain 2 / Single Sheet / 2-Layer Sandwich ...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 / Rubrerythrin, domain 2 - #10 / Rubrerythrin, domain 2 / Single Sheet / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hydrogenase maturation factor HypA
Similarity search - Component
Biological speciesPyrococcus kodakaraensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWatanabe, S. / Arai, T. / Matsumi, R. / Aromi, 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 1.2Jan 1, 2014Group: Database references / Other
Revision 1.3Dec 21, 2016Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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
Water2,252125
1
A: Hydrogenase nickel incorporation protein hypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8052
Polymers15,7401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydrogenase nickel incorporation protein hypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8052
Polymers15,7401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hydrogenase nickel incorporation protein hypA
B: Hydrogenase nickel incorporation protein hypA
hetero molecules

A: Hydrogenase nickel incorporation protein hypA
B: Hydrogenase nickel incorporation protein hypA
hetero molecules

A: Hydrogenase nickel incorporation protein hypA
B: Hydrogenase nickel incorporation protein hypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,83212
Polymers94,4406
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area11290 Å2
ΔGint-66 kcal/mol
Surface area38600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.933, 83.933, 365.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

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Components

#1: Protein Hydrogenase nickel incorporation protein hypA / HypD


Mass: 15739.988 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M HEPES-Na, pH7.4, 1.2M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2005
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21391 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 30.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 1563 / Rsym value: 0.284 / % possible all: 70

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2780349.88 / 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
Rfree0.239 1104 5.2 %RANDOM
Rwork0.215 ---
obs0.215 21362 94.6 %-
all-22628 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.6575 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 80 Å2
Baniso -1Baniso -2Baniso -3
1-12.41 Å20 Å20 Å2
2--12.41 Å20 Å2
3----24.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 2 125 2110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 128 4.8 %
Rwork0.299 2527 -
obs--72 %
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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