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- PDB-4zu3: Halohydrin hydrogen-halide-lyases, HheB -

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Basic information

Entry
Database: PDB / ID: 4zu3
TitleHalohydrin hydrogen-halide-lyases, HheB
ComponentsHalohydrin epoxidase B
KeywordsLYASE
Function / homology
Function and homology information


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
Similarity search - Domain/homology
3-hydroxypentanedinitrile / Halohydrin epoxidase B
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMay 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0Feb 19, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / diffrn_source / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _citation.journal_id_CSD ..._atom_site.occupancy / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.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_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_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_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)152,83215
Polymers151,9416
Non-polymers8919
Water15,421856
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)101,94010
Polymers101,2944
Non-polymers6476
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-81 kcal/mol
Surface area29350 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)101,78310
Polymers101,2944
Non-polymers4896
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area13720 Å2
ΔGint-94 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.910, 215.640, 104.721
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-302-

MG

21A-463-

HOH

31E-456-

HOH

41F-443-

HOH

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Components

#1: Protein
Halohydrin epoxidase B


Mass: 25323.432 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: hheB / Plasmid: pSTT002 / Production host: ESCHERICHIA COLI / Strain (production host): JM109 / References: UniProt: Q46347
#2: Chemical
ChemComp-4SD / 3-hydroxypentanedinitrile


Mass: 110.114 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H6N2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 4000, magnesium chloride, calcium chloride, MES [2-(N-morpholino) ethanesulfonic acid] buffer

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Data collection

DiffractionMean temperature: 95 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: 2.2→50 Å / Num. obs: 71131 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 33.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 8.7 / % possible all: 99.7

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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: 4ZD6

4zd6


Resolution: 2.2→47.013 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3583 5.06 %RANDOM
Rwork0.1627 ---
obs0.165 70879 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10588 0 62 856 11506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410869
X-RAY DIFFRACTIONf_angle_d0.66714747
X-RAY DIFFRACTIONf_dihedral_angle_d14.2286356
X-RAY DIFFRACTIONf_chiral_restr0.0471623
X-RAY DIFFRACTIONf_plane_restr0.0041936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1941-2.2230.33311370.26342408X-RAY DIFFRACTION93
2.223-2.25340.34911460.30292523X-RAY DIFFRACTION99
2.2534-2.28560.35271370.26562521X-RAY DIFFRACTION98
2.2856-2.31970.24181530.19832559X-RAY DIFFRACTION100
2.3197-2.3560.26441410.18082566X-RAY DIFFRACTION100
2.356-2.39460.24091430.17592573X-RAY DIFFRACTION100
2.3946-2.43590.24181180.17432605X-RAY DIFFRACTION100
2.4359-2.48020.22521320.16912590X-RAY DIFFRACTION100
2.4802-2.52790.25341380.17542579X-RAY DIFFRACTION100
2.5279-2.57950.21781260.16792580X-RAY DIFFRACTION100
2.5795-2.63560.26251300.16712606X-RAY DIFFRACTION100
2.6356-2.69690.2431430.17192598X-RAY DIFFRACTION100
2.6969-2.76430.20721280.17192575X-RAY DIFFRACTION100
2.7643-2.8390.22851440.17332591X-RAY DIFFRACTION100
2.839-2.92260.22611380.16732588X-RAY DIFFRACTION100
2.9226-3.01690.19291550.16452580X-RAY DIFFRACTION100
3.0169-3.12470.22831320.17442602X-RAY DIFFRACTION100
3.1247-3.24980.1941490.16472602X-RAY DIFFRACTION100
3.2498-3.39760.2161200.16932601X-RAY DIFFRACTION100
3.3976-3.57670.19721330.16032615X-RAY DIFFRACTION100
3.5767-3.80070.19821340.14542591X-RAY DIFFRACTION99
3.8007-4.0940.1651660.13332587X-RAY DIFFRACTION100
4.094-4.50570.13851420.12092648X-RAY DIFFRACTION100
4.5057-5.1570.1631220.11752656X-RAY DIFFRACTION100
5.157-6.49450.16811410.14982678X-RAY DIFFRACTION100
6.4945-47.02350.20831350.16682674X-RAY DIFFRACTION96

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