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- PDB-4z9f: Halohydrin hydrogen-halide-lyase, HheA -

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Basic information

Entry
Database: PDB / ID: 4z9f
TitleHalohydrin hydrogen-halide-lyase, HheA
ComponentsHalohydrin epoxidase A
KeywordsLYASE
Function / homologyoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Halohydrin epoxidase A
Function and homology information
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWatanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Yohda, M. / Odaka, M.
CitationJournal: Proteins / Year: 2015
Title: Crystal structures of halohydrin hydrogen-halide-lyases from Corynebacterium sp. N-1074
Authors: Watanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Yohda, M. / Odaka, M.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Halohydrin epoxidase A
B: Halohydrin epoxidase A
C: Halohydrin epoxidase A
D: Halohydrin epoxidase A
E: Halohydrin epoxidase A
F: Halohydrin epoxidase A
G: Halohydrin epoxidase A
H: Halohydrin epoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,10816
Polymers211,8248
Non-polymers2848
Water24,1221339
1
A: Halohydrin epoxidase A
B: Halohydrin epoxidase A
C: Halohydrin epoxidase A
D: Halohydrin epoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0548
Polymers105,9124
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-123 kcal/mol
Surface area33140 Å2
MethodPISA
2
E: Halohydrin epoxidase A
F: Halohydrin epoxidase A
G: Halohydrin epoxidase A
H: Halohydrin epoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0548
Polymers105,9124
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-120 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.818, 59.882, 133.734
Angle α, β, γ (deg.)85.39, 83.11, 80.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Halohydrin epoxidase A


Mass: 26478.053 Da / Num. of mol.: 8 / Mutation: T34S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: hheA / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5alpha / References: UniProt: Q46346
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: polyethylene glycol 4000, calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 168566 / % possible obs: 92.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.9 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX(1.10-2152-000)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zmo

1zmo


Resolution: 1.75→29.139 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 8453 5.02 %RANDOM
Rwork0.1891 ---
obs0.1911 168418 92.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14928 0 8 1339 16275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715280
X-RAY DIFFRACTIONf_angle_d0.87820834
X-RAY DIFFRACTIONf_dihedral_angle_d22.5449230
X-RAY DIFFRACTIONf_chiral_restr0.0562349
X-RAY DIFFRACTIONf_plane_restr0.0072781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.29312730.26274889X-RAY DIFFRACTION84
1.7699-1.79070.33342890.26215131X-RAY DIFFRACTION89
1.7907-1.81250.34152710.24755225X-RAY DIFFRACTION89
1.8125-1.83550.29882800.25175321X-RAY DIFFRACTION93
1.8355-1.85960.32213020.24995360X-RAY DIFFRACTION92
1.8596-1.88510.29812670.23515405X-RAY DIFFRACTION93
1.8851-1.9120.28343130.23295352X-RAY DIFFRACTION93
1.912-1.94060.28082720.22845312X-RAY DIFFRACTION92
1.9406-1.97090.27762600.22715422X-RAY DIFFRACTION93
1.9709-2.00320.28352690.23215366X-RAY DIFFRACTION92
2.0032-2.03770.29932900.22435369X-RAY DIFFRACTION93
2.0377-2.07480.26193140.22165265X-RAY DIFFRACTION92
2.0748-2.11470.25452930.20455294X-RAY DIFFRACTION92
2.1147-2.15780.2642690.20845337X-RAY DIFFRACTION92
2.1578-2.20470.27972750.20655343X-RAY DIFFRACTION92
2.2047-2.2560.24882690.20175296X-RAY DIFFRACTION92
2.256-2.31240.262960.2045247X-RAY DIFFRACTION91
2.3124-2.37490.23342800.19715266X-RAY DIFFRACTION91
2.3749-2.44470.25582550.19465326X-RAY DIFFRACTION91
2.4447-2.52360.25172640.20345226X-RAY DIFFRACTION90
2.5236-2.61370.24312730.20185252X-RAY DIFFRACTION90
2.6137-2.71830.23162760.20245259X-RAY DIFFRACTION90
2.7183-2.84190.23612600.20455263X-RAY DIFFRACTION91
2.8419-2.99160.27212550.20655278X-RAY DIFFRACTION91
2.9916-3.17880.23992820.20225320X-RAY DIFFRACTION92
3.1788-3.42390.24562980.18945385X-RAY DIFFRACTION94
3.4239-3.76780.19253380.16865533X-RAY DIFFRACTION96
3.7678-4.31150.17463120.14685699X-RAY DIFFRACTION98
4.3115-5.42630.1612630.13525774X-RAY DIFFRACTION99
5.4263-29.14310.16472950.15245450X-RAY DIFFRACTION95

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