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- PDB-1cqw: NAI COCRYSTALLISED WITH HALOALKANE DEHALOGENASE FROM A RHODOCOCCU... -

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Basic information

Entry
Database: PDB / ID: 1cqw
TitleNAI COCRYSTALLISED WITH HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES
ComponentsHALOALKANE DEHALOGENASE; 1-CHLOROHEXANE HALIDOHYDROLASE
KeywordsHYDROLASE / A/B HYDROLASE FOLD / DEHALOGENASE I-S BOND
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsNewman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C.
CitationJournal: Biochemistry / Year: 1999
Title: Haloalkane dehalogenases: structure of a Rhodococcus enzyme.
Authors: Newman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C.
History
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE; 1-CHLOROHEXANE HALIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5883
Polymers33,3341
Non-polymers2542
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.550, 79.230, 42.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HALOALKANE DEHALOGENASE; 1-CHLOROHEXANE HALIDOHYDROLASE


Mass: 33334.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COCRYSTALLIZED WITH NAI / Source: (gene. exp.) Rhodococcus sp. (bacteria) / Plasmid: PTRCHIS / Production host: Escherichia coli (E. coli) / References: UniProt: P59336, haloalkane dehalogenase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20-25% PEG 1.5K, 0.1M MES pH 5.5 0.3M NaAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMTris-SO41drop
31 mMEDTA1drop
4150 mMammonium sulfate1drop
525 %PEG15001reservoir
60.1 MMES1reservoir
70.3 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.5→12.9 Å / Num. all: 222118 / Num. obs: 47965 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.6
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.154 / Num. unique all: 5826 / % possible all: 78.6
Reflection
*PLUS
Num. measured all: 222118 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 75.6 %

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CNSphasing
RefinementResolution: 1.5→12.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1371216.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2350 5 %RANDOM
Rwork0.176 ---
obs0.176 46900 91.9 %-
Displacement parametersBiso mean: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.5→12.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 2 394 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it0.141.5
X-RAY DIFFRACTIONc_mcangle_it0.252
X-RAY DIFFRACTIONc_scbond_it0.072
X-RAY DIFFRACTIONc_scangle_it0.132.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.207 383 5.4 %
Rwork0.188 6694 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175 / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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