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- PDB-5esr: Crystal structure of haloalkane dehalogenase (DccA) from Caulobac... -

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Basic information

Entry
Database: PDB / ID: 5esr
TitleCrystal structure of haloalkane dehalogenase (DccA) from Caulobacter crescentus
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / Alpha/beta hydrolase family / Epoxide hydrolase-like / 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
: / Haloalkane dehalogenase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.476 Å
AuthorsMalashkevich, V.N. / Toro, R. / Mundorff, E.C. / Almo, S.C.
CitationJournal: Protein Sci. / Year: 2016
Title: Biochemical characterization of two haloalkane dehalogenases: DccA from Caulobacter crescentus and DsaA from Saccharomonospora azurea.
Authors: Carlucci, L. / Zhou, E. / Malashkevich, V.N. / Almo, S.C. / Mundorff, E.C.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_prerelease_seq ...citation / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct / struct_conn
Item: _audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _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
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,45910
Polymers34,0211
Non-polymers4389
Water7,981443
1
A: Haloalkane dehalogenase
hetero molecules

A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,91820
Polymers68,0422
Non-polymers87518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3720 Å2
ΔGint-181 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.377, 79.643, 94.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

21A-773-

HOH

31A-905-

HOH

41A-937-

HOH

51A-943-

HOH

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34021.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: dhmA, CC_1175 / Plasmid: PJ401express / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q9A919, haloalkane dehalogenase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005 M Cobalt chloride, 0.005 Magnesium chloride, 0.005 Cadmium chloride, 0.005 Nickel chloride, 0.1 M HEPES:NaOH, pH 7.5, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.476→94.766 Å / Num. all: 50696 / Num. obs: 50696 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 8.68 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.119 / Rsym value: 0.11 / Net I/av σ(I): 5.542 / Net I/σ(I): 19.1 / Num. measured all: 739115
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.476-1.5614.50.5631.310646873300.1570.5635.8100
1.56-1.6514.60.411.810125869350.1140.417.7100
1.65-1.7614.70.2912.69564265230.0810.29110.4100
1.76-1.9114.70.1963.88925960780.0550.19614.4100
1.91-2.0914.70.1385.48292156300.0390.13819.4100
2.09-2.3314.70.1027.17509351130.0290.10225.6100
2.33-2.6914.70.08686601245010.0240.08629.7100
2.69-3.314.60.0689.25642938580.0190.06835.3100
3.3-4.6714.30.056114291830050.0160.05644100
4.67-94.76613.40.05211.62311517230.0160.05244.199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å56.22 Å
Translation2.5 Å56.22 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XT0

2xt0


Resolution: 1.476→47.383 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1488 2572 5.08 %
Rwork0.1262 92553 -
obs0.1273 50696 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.48 Å2 / Biso mean: 12.6575 Å2 / Biso min: 3.6 Å2
Refinement stepCycle: final / Resolution: 1.476→47.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 9 443 2859
Biso mean--10.63 27.39 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082530
X-RAY DIFFRACTIONf_angle_d1.2623461
X-RAY DIFFRACTIONf_chiral_restr0.072372
X-RAY DIFFRACTIONf_plane_restr0.007458
X-RAY DIFFRACTIONf_dihedral_angle_d12.305919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4761-1.49290.17121630.182930603223100
1.4929-1.51050.1691730.174931103283100
1.5105-1.52890.1881750.166231033278100
1.5289-1.54820.19981610.166630713232100
1.5482-1.56860.19081380.159730983236100
1.5686-1.59010.17451790.155330413220100
1.5901-1.61280.16281650.151131193284100
1.6128-1.63690.17651850.1430673252100
1.6369-1.66250.16181790.141630533232100
1.6625-1.68970.14851960.130330593255100
1.6897-1.71890.15321730.130630873260100
1.7189-1.75010.12931500.123231313281100
1.7501-1.78380.15651730.133930193192100
1.7838-1.82020.18151870.119531073294100
1.8202-1.85980.14571750.123730433218100
1.8598-1.9030.14181630.11630943257100
1.903-1.95060.14522020.113930453247100
1.9506-2.00340.14371420.118631213263100
2.0034-2.06230.14841560.11630783234100
2.0623-2.12890.13781740.111431103284100
2.1289-2.2050.11791400.110131193259100
2.205-2.29330.13391300.109431023232100
2.2933-2.39760.13591750.113330713246100
2.3976-2.5240.13861410.111930993240100
2.524-2.68210.14791720.114331193291100
2.6821-2.88920.14721650.120530513216100
2.8892-3.17990.16691760.122830843260100
3.1799-3.63990.13991660.123530913257100
3.6399-4.58530.13631530.112131113264100
4.5853-47.40740.13521310.14633090322199
Refinement TLS params.Method: refined / Origin x: 23.8632 Å / Origin y: 21.3225 Å / Origin z: 10.6223 Å
111213212223313233
T0.0477 Å2-0.0068 Å20.0003 Å2-0.0579 Å2-0.0047 Å2--0.0297 Å2
L0.3925 °2-0.3746 °20.0931 °2-0.8987 °2-0.1682 °2--0.3777 °2
S-0.0136 Å °-0.0244 Å °-0.0091 Å °0.0604 Å °0.0035 Å °0.0023 Å °0.0101 Å °0.0099 Å °0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 308
2X-RAY DIFFRACTION1allA401 - 409
3X-RAY DIFFRACTION1allS1 - 473

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