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- PDB-1zrm: CRYSTAL STRUCTURE OF THE REACTION INTERMEDIATE OF L-2-HALOACID DE... -

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Basic information

Entry
Database: PDB / ID: 1zrm
TitleCRYSTAL STRUCTURE OF THE REACTION INTERMEDIATE OF L-2-HALOACID DEHALOGENASE WITH 2-CHLORO-N-BUTYRATE
ComponentsL-2-HALOACID DEHALOGENASE
KeywordsDEHALOGENASE / HYDROLASE
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...L-2-Haloacid dehalogenase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
butanoic acid / (S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, Y.-F. / Hata, Y. / Fujii, T. / Hisano, T. / Nishihara, M. / Kurihara, T. / Esaki, N.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
Authors: Li, Y.F. / Hata, Y. / Fujii, T. / Hisano, T. / Nishihara, M. / Kurihara, T. / Esaki, N.
History
DepositionMar 3, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 31, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-2-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2802
Polymers26,1921
Non-polymers881
Water91951
1
A: L-2-HALOACID DEHALOGENASE
hetero molecules

A: L-2-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5594
Polymers52,3832
Non-polymers1762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3330 Å2
ΔGint-10 kcal/mol
Surface area17400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.990, 62.940, 50.950
Angle α, β, γ (deg.)90.00, 122.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-2-HALOACID DEHALOGENASE


Mass: 26191.588 Da / Num. of mol.: 1 / Mutation: S175A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: YL / Gene: L-DEX_YL / Plasmid: PBA501 / Gene (production host): L-DEX_YL / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q53464, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlenzyme1drop
250 mMpotassium dehydrogenphosphate1reservoir
315 %(w/v)PEG80001reservoir
41 %(v/v)n-propanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 26, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→48.62 Å / Num. obs: 14454 / % possible obs: 87.1 % / Observed criterion σ(I): 1 / Redundancy: 2.58 % / Biso Wilson estimate: 19.92 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.78→2 Å / Redundancy: 2.78 % / Rmerge(I) obs: 0.334 / % possible all: 74.9
Reflection
*PLUS
Num. measured all: 37221
Reflection shell
*PLUS
% possible obs: 74.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISIICdata reduction
R-AXISIICdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JUD

1jud


Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1273 10.4 %RANDOM
Rwork0.204 ---
obs0.204 12280 75.9 %-
Displacement parametersBiso mean: 42.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 6 51 1803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.466 69 9.83 %
Rwork0.39 702 -
obs--38.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARA.WATERTOPO.WATER
X-RAY DIFFRACTION3PARA.CPDTOPO.CPD
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor obs: 0.39

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