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- PDB-4zd6: Halohydrin hydrogen-halide-lyase, HheB -

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Basic information

Entry
Database: PDB / ID: 4zd6
TitleHalohydrin hydrogen-halide-lyase, HheB
ComponentsHalohydrin epoxidase B
KeywordsLYASE
Function / homologyEnoyl-(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 / metal ion binding / Alpha Beta / Halohydrin epoxidase B
Function and homology information
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 17, 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,42116
Polymers151,9416
Non-polymers48110
Water18,8261045
1
A: Halohydrin epoxidase B
B: Halohydrin epoxidase B
C: Halohydrin epoxidase B
D: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6319
Polymers101,2944
Non-polymers3375
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14580 Å2
ΔGint-120 kcal/mol
Surface area29280 Å2
MethodPISA
2
E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules

E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,58114
Polymers101,2944
Non-polymers28810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area14320 Å2
ΔGint-136 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.484, 216.380, 104.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-304-

MG

21E-476-

HOH

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Components

#1: Protein
Halohydrin epoxidase B


Mass: 25323.432 Da / Num. of mol.: 6 / Fragment: UNP residues 11-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: hheB / Plasmid: pSTT002 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q46347
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1045 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: polyethylene glycol 4000, magnesium chloride, 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: 1.6→50 Å / Num. obs: 158218 / % possible obs: 87.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.86 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10-2152-000)refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→35.31 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 7926 5.02 %RANDOM
Rwork0.175 ---
obs0.1766 157936 87.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10596 0 21 1045 11662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610853
X-RAY DIFFRACTIONf_angle_d0.79114746
X-RAY DIFFRACTIONf_dihedral_angle_d14.7586353
X-RAY DIFFRACTIONf_chiral_restr0.0531620
X-RAY DIFFRACTIONf_plane_restr0.0061943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.61810.23653020.1975260X-RAY DIFFRACTION93
1.6181-1.63720.25332920.18795603X-RAY DIFFRACTION99
1.6372-1.65710.23153400.18985580X-RAY DIFFRACTION99
1.6571-1.67810.20833000.17975626X-RAY DIFFRACTION100
1.6781-1.70020.22533210.17425628X-RAY DIFFRACTION100
1.7002-1.72350.21573010.1675687X-RAY DIFFRACTION100
1.7235-1.74810.21952700.16695664X-RAY DIFFRACTION100
1.7481-1.77420.22652880.1665657X-RAY DIFFRACTION100
1.7742-1.80190.21893130.16755673X-RAY DIFFRACTION100
1.8019-1.83140.21632920.16855647X-RAY DIFFRACTION100
1.8314-1.8630.23472760.18375697X-RAY DIFFRACTION100
1.863-1.89690.32371550.25582911X-RAY DIFFRACTION91
1.8969-1.93340.5996380.51741078X-RAY DIFFRACTION60
1.9334-1.97280.33812500.27434772X-RAY DIFFRACTION92
1.9728-2.01570.21582900.18215659X-RAY DIFFRACTION100
2.0157-2.06260.19792890.16795696X-RAY DIFFRACTION100
2.0626-2.11420.21552810.16525711X-RAY DIFFRACTION100
2.1142-2.17140.19543110.16815699X-RAY DIFFRACTION100
2.1714-2.23520.22111530.19552664X-RAY DIFFRACTION88
2.2352-2.30740.2281650.20721112X-RAY DIFFRACTION80
2.3074-2.38980.19012820.17185730X-RAY DIFFRACTION100
2.3898-2.48550.20553240.16665662X-RAY DIFFRACTION100
2.4855-2.59860.18933360.17215650X-RAY DIFFRACTION100
2.5986-2.73550.20213060.17225697X-RAY DIFFRACTION100
2.7355-2.90680.23352910.17445728X-RAY DIFFRACTION99
2.9068-3.13120.19112860.17485717X-RAY DIFFRACTION99
3.1312-3.4460.21532930.17245728X-RAY DIFFRACTION99
3.446-3.94410.17321200.16592238X-RAY DIFFRACTION44
3.9441-4.96690.15272580.13825251X-RAY DIFFRACTION96
4.9669-35.31880.17473030.1575585X-RAY DIFFRACTION93

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