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- PDB-1nzy: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE FROM PSEUDOMONAS SP. STRA... -

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Basic information

Entry
Database: PDB / ID: 1nzy
Title4-CHLOROBENZOYL COENZYME A DEHALOGENASE FROM PSEUDOMONAS SP. STRAIN CBS-3
Components(4-CHLOROBENZOYL COENZYME A ...) x 2
KeywordsLYASE
Function / homology
Function and homology information


4-chlorobenzoyl-CoA dehalogenase / 4-chlorobenzoyl-CoA dehalogenase activity / coenzyme A metabolic process
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-HYDROXYBENZOYL COENZYME A / PHOSPHATE ION / : / 4-chlorobenzoyl coenzyme A dehalogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
Pseudomonas sp. CBS3 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBenning, M.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1996
Title: Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: an enzyme catalyst generated via adaptive mutation.
Authors: Benning, M.M. / Taylor, K.L. / Liu, R.-.Q. / Yang, G. / Xiang, H. / Wesenberg, G. / Dunaway-Mariano, D. / Holden, H.M.
History
DepositionApr 2, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.ptnr2_auth_asym_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
B: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
C: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,69912
Polymers89,6963
Non-polymers3,0029
Water10,773598
1
A: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
B: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
C: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
hetero molecules

A: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
B: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
C: 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,39724
Polymers179,3936
Non-polymers6,00518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-111 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.800, 102.400, 90.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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4-CHLOROBENZOYL COENZYME A ... , 2 types, 3 molecules ACB

#1: Protein 4-CHLOROBENZOYL COENZYME A DEHALOGENASE / DEHALOGENASE


Mass: 29898.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: CBS-3 / Production host: Escherichia coli (E. coli) / References: PIR: A42560, UniProt: A5JTM5*PLUS, EC: 3.8.1.6
#2: Protein 4-CHLOROBENZOYL COENZYME A DEHALOGENASE / DEHALOGENASE


Mass: 29899.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. CBS3 (bacteria) / Strain: CBS-3 / Production host: Escherichia coli (E. coli) / References: PIR: A42560, UniProt: A5JTM5*PLUS, EC: 3.8.1.6

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Non-polymers , 5 types, 607 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BCA / 4-HYDROXYBENZOYL COENZYME A


Mass: 887.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H40N7O18P3S
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9 / Method: batch method / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %PEG800011
2200 mMpotassium chloride11
350 mMCHES11
45 mM11NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30.3 Å / % possible obs: 98 % / Rmerge(I) obs: 0.036

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementRfactor Rwork: 0.188 / Highest resolution: 1.8 Å / Details: TNT
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 175 598 7050
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.31

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