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- PDB-3wjr: crystal structure of HypE in complex with a nucleotide -

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Basic information

Entry
Database: PDB / ID: 3wjr
Titlecrystal structure of HypE in complex with a nucleotide
ComponentsHydrogenase expression/formation protein HypE
KeywordsLYASE / [NiFe]hydrogenase maturation
Function / homology
Function and homology information


protein maturation / ATP binding / metal ion binding
Similarity search - Function
Carbamoyl dehydratase HypE / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Carbamoyl dehydratase HypE / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BENZAMIDINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Hydrogenase expression/formation protein HypE
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.864 Å
AuthorsTominaga, T. / Watanabe, S. / Miki, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation
Authors: Tominaga, T. / Watanabe, S. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionOct 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Hydrogenase expression/formation protein HypE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,39513
Polymers35,9541
Non-polymers1,44112
Water5,188288
1
A: Hydrogenase expression/formation protein HypE
hetero molecules

A: Hydrogenase expression/formation protein HypE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,79026
Polymers71,9092
Non-polymers2,88124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12450 Å2
ΔGint-145 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.657, 102.657, 105.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hydrogenase expression/formation protein HypE


Mass: 35954.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1993 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII7

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Non-polymers , 8 types, 300 molecules

#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MES-NaOH, 1.4-1.55M ammonium sulfate, 1.7%(v/v) polyethylene glycol 400, 6%(v/v) glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 / Detector: PIXEL / Date: Jan 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 47673 / Num. obs: 47503 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 29.76 Å2 / Rsym value: 0.071 / Net I/σ(I): 22.14
Reflection shellResolution: 1.86→1.98 Å / Redundancy: 13 % / Mean I/σ(I) obs: 4.46 / Num. unique all: 7564 / Rsym value: 0.66 / % possible all: 98

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYT

3vyt


Resolution: 1.864→46.998 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8785 / SU ML: 0.16 / σ(F): 1.36 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 2367 4.98 %RANDOM
Rwork0.1727 ---
obs0.1741 47503 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.89 Å2 / Biso mean: 32.727 Å2 / Biso min: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.864→46.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 90 288 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072655
X-RAY DIFFRACTIONf_angle_d1.1233602
X-RAY DIFFRACTIONf_chiral_restr0.078415
X-RAY DIFFRACTIONf_plane_restr0.005466
X-RAY DIFFRACTIONf_dihedral_angle_d13.512983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8643-1.90240.24511290.23042461259094
1.9024-1.94380.22751460.208926152761100
1.9438-1.9890.24781350.190626292764100
1.989-2.03870.19841450.176226092754100
2.0387-2.09380.21281510.181626262777100
2.0938-2.15540.20721340.176626122746100
2.1554-2.2250.2291360.17426502786100
2.225-2.30450.19981430.169626462789100
2.3045-2.39680.18421400.162626092749100
2.3968-2.50590.18161330.172726672800100
2.5059-2.6380.18161320.165726602792100
2.638-2.80320.20781190.174926682787100
2.8032-3.01960.2111430.182626792822100
3.0196-3.32350.1911720.175626532825100
3.3235-3.80420.17481250.162827222847100
3.8042-4.79210.18041510.146427242875100
4.7921-47.01340.22841330.191429063039100

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