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- PDB-2rb9: Crystal structure of E.coli HypE -

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Basic information

Entry
Database: PDB / ID: 2rb9
TitleCrystal structure of E.coli HypE
ComponentsHypE protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hydrogenase maturation / dimer / enzyme / BSGI / Montreal-Kingston Bacterial Structural Genomics Initiative
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases
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
Carbamoyl dehydratase / :
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsAsinas, A.E. / Rangarajan, E.S. / Min, T. / Matte, A. / Proteau, A. / Munger, C. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2008
Title: Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF.
Authors: Rangarajan, E.S. / Asinas, A. / Proteau, A. / Munger, C. / Baardsnes, J. / Iannuzzi, P. / Matte, A. / Cygler, M.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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: HypE protein
B: HypE protein
C: HypE protein
D: HypE protein


Theoretical massNumber of molelcules
Total (without water)140,5654
Polymers140,5654
Non-polymers00
Water12,863714
1
A: HypE protein
B: HypE protein


Theoretical massNumber of molelcules
Total (without water)70,2832
Polymers70,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
MethodPISA
2
C: HypE protein
D: HypE protein


Theoretical massNumber of molelcules
Total (without water)70,2832
Polymers70,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.574, 72.303, 112.607
Angle α, β, γ (deg.)90.000, 115.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

DetailsAuthors state that the biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D).

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Components

#1: Protein
HypE protein /


Mass: 35141.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Species: Escherichia coli / Strain: O157:H7, EDL933, Sakai, RIMD 0509952, EHEC / Gene: hypE, ECs3586 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7ABB2, UniProt: A0A0H3JHA1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.6M Na/K phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2007
RadiationMonochromator: Kohzu HLD-4 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 196364 / % possible obs: 81.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Χ2: 0.741 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.661.20.59622460.2839.4
1.66-1.721.60.58788160.28336.9
1.72-1.82.40.577192260.30880.1
1.8-1.93.40.481232880.31897.3
1.9-2.023.70.284235930.32598.5
2.02-2.173.70.168237050.37998.7
2.17-2.393.70.114238260.51999.1
2.39-2.743.80.08238760.75899.3
2.74-3.453.80.053239761.2599.4
3.45-503.70.037238121.76797.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å43.72 Å
Translation1.96 Å43.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2I6R

2i6r


Resolution: 2→43.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.798 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The N-terminal serine, resulting from the vector sequence, was only modelled in chain D, and is missing in chains A,B,C due to lack ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The N-terminal serine, resulting from the vector sequence, was only modelled in chain D, and is missing in chains A,B,C due to lack of electron density (see remark 465).
RfactorNum. reflection% reflectionSelection details
Rfree0.208 6153 5 %RANDOM
Rwork0.176 ---
obs0.177 123532 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9854 0 0 714 10568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210065
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.98713799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32151412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01724.73389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.415151683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5191562
X-RAY DIFFRACTIONr_chiral_restr0.0720.21677
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027600
X-RAY DIFFRACTIONr_nbd_refined0.20.24720
X-RAY DIFFRACTIONr_nbtor_refined0.2960.27067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2758
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.234
X-RAY DIFFRACTIONr_mcbond_it1.34836843
X-RAY DIFFRACTIONr_mcangle_it2.163510671
X-RAY DIFFRACTIONr_scbond_it2.20443570
X-RAY DIFFRACTIONr_scangle_it3.5273081
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 443 -
Rwork0.192 8608 -
all-9051 -
obs--98.71 %

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