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- PDB-2i6r: Crystal structure of E. coli HypE, a hydrogenase maturation protein -

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Basic information

Entry
Database: PDB / ID: 2i6r
TitleCrystal structure of E. coli HypE, a hydrogenase maturation protein
ComponentsHypE protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HypE / Hydrogenase Maturation Protein / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


peptidyl-S-carbamoyl-L-cysteine dehydration / Lyases; Carbon-oxygen lyases; Hydro-lyases / protein maturation / lyase activity
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 HypE / :
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsRangarajan, E.S. / Proteau, A. / Iannuzzi, P. / Matte, A. / 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
DepositionAug 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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: HypE protein
B: HypE protein
C: HypE protein
D: HypE protein


Theoretical massNumber of molelcules
Total (without water)140,5654
Polymers140,5654
Non-polymers00
Water7,152397
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 area5110 Å2
ΔGint-19 kcal/mol
Surface area24590 Å2
MethodPISA, PQS
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 area5230 Å2
ΔGint-19 kcal/mol
Surface area24560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)254.757, 71.776, 113.034
Angle α, β, γ (deg.)90.000, 115.120, 90.000
Int Tables number5
Space group name H-MC121

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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: P24193*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 63.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.28 M NaK phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2005 / Details: silicon
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 21.9 / Number: 173055 / Rmerge(I) obs: 0.051 / Χ2: 2.32 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 92233 / % possible obs: 92.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815094.610.0262.4141.9
4.625.8196.210.0342.31.9
4.034.6295.810.0362.4731.9
3.664.0390.210.0492.8141.8
3.43.6690.110.0662.7371.8
3.23.494.810.0842.2271.9
3.043.294.110.1282.1971.9
2.913.0493.710.1712.0331.9
2.82.9192.910.2272.0271.9
2.72.880.410.2611.9941.8
ReflectionResolution: 2.5→50 Å / Num. all: 63144 / Num. obs: 63144 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Χ2: 1.354 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.592.90.30360140.462195.5
2.59-2.693.60.28462860.562199.7
2.69-2.823.60.263290.587199.9
2.82-2.963.90.16463270.658199.9
2.96-3.153.80.1262980.869199.9
3.15-3.393.70.0963331.309199.9
3.39-3.733.80.07563431.818199.7
3.73-4.273.80.05963482.25199.8
4.27-5.383.60.04863782.529199.5
5.38-503.60.03664882.207199.3

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.61 / FOM acentric: 0.6 / FOM centric: 0.83 / Reflection: 49576 / Reflection acentric: 47121 / Reflection centric: 2455
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-38.8320.930.940.8821991907292
4.8-7.70.920.871.5767796281498
3.9-4.80.840.850.884488004444
3.4-3.90.720.720.7780807724356
2.9-3.40.460.460.511501914458561
2.7-2.90.240.240.390518747304

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→43.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.644 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3190 5.1 %RANDOM
Rwork0.193 ---
obs0.193 63142 99.09 %-
all-63142 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.07 Å2
2---0.11 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.51→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9367 0 0 397 9764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229499
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.98212906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84851263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55524.503362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.274151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3831560
X-RAY DIFFRACTIONr_chiral_restr0.0850.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027030
X-RAY DIFFRACTIONr_nbd_refined0.2060.24388
X-RAY DIFFRACTIONr_nbtor_refined0.30.26562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2472
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.218
X-RAY DIFFRACTIONr_mcbond_it0.521.56424
X-RAY DIFFRACTIONr_mcangle_it0.919210024
X-RAY DIFFRACTIONr_scbond_it1.5233350
X-RAY DIFFRACTIONr_scangle_it2.5874.52882
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 210 -
Rwork0.25 4071 -
obs-4281 91.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20432.7619-1.591829.52197.67397.63480.24890.17230.5673-0.3803-0.56191.2894-1.3694-0.53750.3130.13350.1738-0.09350.27050.0440.1657106.920410.46221.0656
210.6193-3.41443.426616.4298.022911.1564-0.0114-0.98820.92020.4074-0.0325-1.5679-0.14071.0040.04390.25740.0222-0.00080.33830.13020.2206114.62720.540931.8548
38.58067.1571.933311.441-1.3258.0606-0.14711.0352-0.9088-0.78340.071-0.13111.39-0.33730.07610.2318-0.04040.05190.3971-0.01240.208639.4835-0.232823.1531
44.4459-4.09934.559511.8183-5.609911.6738-0.2776-1.0693-0.01790.98770.3472-0.42330.442-0.2283-0.06960.1752-0.06150.04520.2851-0.12390.146868.41576.303938.9232
52.76780.13190.95330.47720.03491.15560.00330.0769-0.05910.0582-0.0203-0.00140.00260.2150.017-0.04390.0352-0.04060.02150.0396-0.01171282.404616.347
63.2375-0.76071.29840.6197-0.3490.8738-0.0034-0.12940.06230.0644-0.0131-0.1316-0.05030.10370.0165-0.06320.03130.0305-0.13420.0096-0.068593.60165.614815.0761
70.68890.03350.15441.00280.33363.282-0.0054-0.25540.04950.10690.0111-0.05670.0065-0.3328-0.0056-0.12920.00290.05850.0554-0.033-0.099149.82898.576746.8019
80.74110.05910.24981.1160.53721.91070.0244-0.1072-0.00250.0754-0.02110.07110.0376-0.1083-0.0034-0.1705-0.01260.044-0.23160.0089-0.157158.1954-0.305314.4385
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1813 - 30
22BB1 - 1813 - 30
33CC1 - 1813 - 30
44DD1 - 1813 - 30
55AA19 - 32231 - 334
66BB19 - 32231 - 334
77CC19 - 32231 - 334
88DD19 - 32231 - 334

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