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- PDB-4g9i: Crystal structure of T.kodakarensis HypF -

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Basic information

Entry
Database: PDB / ID: 4g9i
TitleCrystal structure of T.kodakarensis HypF
ComponentsHydrogenase maturation protein HypF
KeywordsTRANSFERASE / Zinc finger / Hydrogenase maturation / ATP binding / Carbamoylation
Function / homology
Function and homology information


protein carbamoylation / Ligases; Forming carbon-sulfur bonds / acylphosphatase activity / carboxyl- or carbamoyltransferase activity / ligase activity / protein maturation / double-stranded RNA binding / zinc ion binding
Similarity search - Function
Carbamoyltransferase, HypF-type / Zinc finger, HypF-type / HypF, Kae1-like domain / HypF finger / HypF Kae1-like domain / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase ...Carbamoyltransferase, HypF-type / Zinc finger, HypF-type / HypF, Kae1-like domain / HypF finger / HypF Kae1-like domain / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / DHBP synthase RibB-like alpha/beta domain superfamily / Acylphosphatase-like domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Carbamoyltransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.5 Å
AuthorsTominaga, T. / Watanabe, S. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.
Authors: Tominaga, T. / Watanabe, S. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase maturation protein HypF
B: Hydrogenase maturation protein HypF
C: Hydrogenase maturation protein HypF
D: Hydrogenase maturation protein HypF
E: Hydrogenase maturation protein HypF
F: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,02724
Polymers525,8506
Non-polymers1,17718
Water0
1
A: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8384
Polymers87,6421
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8384
Polymers87,6421
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8384
Polymers87,6421
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8384
Polymers87,6421
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8384
Polymers87,6421
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Hydrogenase maturation protein HypF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8384
Polymers87,6421
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)265.810, 265.810, 693.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Hydrogenase maturation protein HypF


Mass: 87641.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: hypF, TK1997 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / 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: 6.73 Å3/Da / Density % sol: 81.71 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1M Tris-HCl, 3.7M sodium chloride, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.976 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 143223 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rsym value: 0.174 / Net I/σ(I): 12.6
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.689 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 4.5→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 13105382.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3 7219 5 %RANDOM
Rwork0.279 ---
obs0.279 143223 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 116.973 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 186.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.18 Å20 Å20 Å2
2--8.18 Å20 Å2
3----16.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.75 Å0.69 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å1.03 Å
Refinement stepCycle: LAST / Resolution: 4.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36047 0 18 0 36065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.821.5
X-RAY DIFFRACTIONc_mcangle_it6.772
X-RAY DIFFRACTIONc_scbond_it4.72
X-RAY DIFFRACTIONc_scangle_it7.912.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 4.5→4.77 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 1067 4.9 %
Rwork0.376 20915 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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