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- PDB-2z1t: Crystal Structure of Hydrogenase Maturation Protein HypE -

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Basic information

Entry
Database: PDB / ID: 2z1t
TitleCrystal Structure of Hydrogenase Maturation Protein HypE
ComponentsHydrogenase expression/formation protein HypE
KeywordsLYASE / alpha-beta fold / beta barrel
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
Hydrogenase expression/formation protein HypE
Similarity search - Component
Biological speciesDesulfovibrio vulgaris subsp. vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShomura, Y. / Higuchi, Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Hydrogenase Maturation Protein HypE in the Apo and ATP-bound Forms
Authors: Shomura, Y. / Komori, H. / Miyabe, N. / Tomiyama, M. / Shibata, N. / Higuchi, Y.
History
DepositionMay 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase expression/formation protein HypE


Theoretical massNumber of molelcules
Total (without water)36,0961
Polymers36,0961
Non-polymers00
Water73941
1
A: Hydrogenase expression/formation protein HypE

A: Hydrogenase expression/formation protein HypE


Theoretical massNumber of molelcules
Total (without water)72,1922
Polymers72,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4510 Å2
ΔGint-18 kcal/mol
Surface area24030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.400, 67.400, 183.988
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hydrogenase expression/formation protein HypE


Mass: 36096.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris (bacteria)
Species: Desulfovibrio vulgaris / Strain: Hildenborough / Gene: hypE / Plasmid: pPROExHTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72F88
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.35 Å3/Da / Density % sol: 63.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, 25% MPD, pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 8, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→33.1 Å / Num. all: 15579 / Num. obs: 15436 / % possible obs: 98.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2 / Num. unique all: 1497 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→33.1 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 23.924 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27827 776 5 %RANDOM
Rwork0.22853 ---
obs0.23089 14627 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.263 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å21.4 Å20 Å2
2--2.79 Å20 Å2
3----4.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 41 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222401
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9873255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97823.60897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1961521
X-RAY DIFFRACTIONr_chiral_restr0.1070.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021804
X-RAY DIFFRACTIONr_nbd_refined0.2520.21133
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.24
X-RAY DIFFRACTIONr_mcbond_it0.6671.51616
X-RAY DIFFRACTIONr_mcangle_it1.19522530
X-RAY DIFFRACTIONr_scbond_it1.5993840
X-RAY DIFFRACTIONr_scangle_it2.6554.5725
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 57 -
Rwork0.308 1030 -
obs--97.58 %
Refinement TLS params.Method: refined / Origin x: 8.492 Å / Origin y: 24.8165 Å / Origin z: -15.8975 Å
111213212223313233
T-0.2942 Å20.0324 Å20.0022 Å2-0.2866 Å20.0253 Å2---0.0395 Å2
L1.3021 °2-0.0568 °21.2518 °2-0.7093 °2-0.4357 °2--4.3818 °2
S-0.0754 Å °0.6277 Å °0.0319 Å °0.2078 Å °0.1128 Å °-0.0604 Å °0.2159 Å °-0.03 Å °-0.0373 Å °

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