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- PDB-4mj3: Haloalkane dehalogenase DmrA from Mycobacterium rhodesiae JS60 -

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Basic information

Entry
Database: PDB / ID: 4mj3
TitleHaloalkane dehalogenase DmrA from Mycobacterium rhodesiae JS60
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Dehalogenase
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
Similarity search - Function
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
: / Haloalkane dehalogenase
Similarity search - Component
Biological speciesMycobacterium rhodesiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsFung, H. / Gadd, M.S. / Guss, J.M. / Matthews, J.M.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes.
Authors: Fung, H.K. / Gadd, M.S. / Drury, T.A. / Cheung, S. / Guss, J.M. / Coleman, N.V. / Matthews, J.M.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_auth_seq_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.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Haloalkane dehalogenase
B: Haloalkane dehalogenase
C: Haloalkane dehalogenase
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,50514
Polymers143,1284
Non-polymers37610
Water18,9341051
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8182
Polymers35,7821
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9355
Polymers35,7821
Non-polymers1534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8573
Polymers35,7821
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8964
Polymers35,7821
Non-polymers1143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.220, 79.079, 95.761
Angle α, β, γ (deg.)90.000, 92.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA1 - 3011 - 301
21ASNASNBB1 - 3011 - 301
12ASNASNAA1 - 3011 - 301
22ASNASNCC1 - 3011 - 301
13ASNASNAA1 - 3011 - 301
23ASNASNDD1 - 3011 - 301
14ARGARGBB1 - 3031 - 303
24ARGARGCC1 - 3031 - 303
15ARGARGBB1 - 3031 - 303
25ARGARGDD1 - 3031 - 303
16ARGARGCC1 - 3031 - 303
26ARGARGDD1 - 3031 - 303

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Haloalkane dehalogenase


Mass: 35782.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium rhodesiae (bacteria) / Strain: JS60 / Gene: MycrhDRAFT_3907 / Production host: Escherichia coli (E. coli) / References: UniProt: G4I2J6, haloalkane dehalogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1051 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M bis-Tris propane, pH 6.5, 0.2 M potassium thiocyanate, 16% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2012
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 134710 / Num. obs: 134710 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.73 Å / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERautosolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→48.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.58 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 6791 5.1 %RANDOM
Rwork0.1653 ---
obs0.1665 134419 97.24 %-
all-134419 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.6 Å2 / Biso mean: 17.2792 Å2 / Biso min: 7.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0.1 Å2
2---0.46 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9219 0 10 1051 10280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199531
X-RAY DIFFRACTIONr_bond_other_d0.0060.028740
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9613035
X-RAY DIFFRACTIONr_angle_other_deg1.073320090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41551215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2423.27422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.386151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1921564
X-RAY DIFFRACTIONr_chiral_restr0.0710.21403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111005
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022219
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A181810.06
12B181810.06
21A182390.05
22C182390.05
31A182940.05
32D182940.05
41B181510.07
42C181510.07
51B183420.06
52D183420.06
61C182550.06
62D182550.06
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 508 -
Rwork0.25 9110 -
all-9618 -
obs-9618 94.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4371-0.03230.06190.61680.20510.82640.00250.0326-0.0054-0.07230.0139-0.0621-0.08830.0291-0.01640.01470.00170.00740.03740.00230.00761.005841.8159-11.5548
21.26630.0715-0.10160.4154-0.0380.780.0110.0121-0.0871-0.0123-0.01820.02140.06030.00240.00720.00520.0014-0.00150.0265-0.00560.008224.565243.410913.5115
30.6339-0.0331-0.07460.48030.04590.6954-0.00630.02650.0459-0.01550.01220.01450.0282-0.0319-0.00590.0097-0.0109-0.00970.0551-0.00070.017162.35368.208436.0932
40.8107-0.22990.19590.6103-0.07030.80950.0191-0.0028-0.03630.0134-0.00780.0319-0.03390.0134-0.01130.0064-0.0135-0.00510.05910.01180.013666.424245.971534.8907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 302
2X-RAY DIFFRACTION2B1 - 303
3X-RAY DIFFRACTION3C1 - 303
4X-RAY DIFFRACTION4D1 - 303

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