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- PDB-3e99: Crystal structure of the beta subunit of the benzoate 1,2-dioxyge... -

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Basic information

Entry
Database: PDB / ID: 3.0E+99
TitleCrystal structure of the beta subunit of the benzoate 1,2-dioxygenase (benb, bmaa0186) from burkholderia mallei atcc 23344 at 1.90 A resolution
ComponentsBenzoate 1,2-dioxygenase beta subunit
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


benzoate 1,2-dioxygenase / benzoate 1,2-dioxygenase activity / : / 3-phenylpropionate catabolic process
Similarity search - Function
Benzoate 1,2-dioxygenase, small subunit / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Benzoate 1,2-dioxygenase beta subunit / Benzoate 1,2-dioxygenase beta subunit
Similarity search - Component
Biological speciesBurkholderia mallei ATCC 23344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of the beta subunit of benzoate 1,2-dioxygenase (YP_105014.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benzoate 1,2-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4122
Polymers19,3531
Non-polymers591
Water2,504139
1
A: Benzoate 1,2-dioxygenase beta subunit
hetero molecules

A: Benzoate 1,2-dioxygenase beta subunit
hetero molecules

A: Benzoate 1,2-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2376
Polymers58,0593
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4830 Å2
ΔGint-8 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.953, 58.953, 167.073
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-174-

HOH

21A-188-

HOH

31A-197-

HOH

41A-213-

HOH

51A-239-

HOH

61A-243-

HOH

71A-256-

HOH

81A-275-

HOH

91A-283-

HOH

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Components

#1: Protein Benzoate 1,2-dioxygenase beta subunit


Mass: 19353.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia mallei ATCC 23344 (bacteria)
Gene: YP_105014.1, benB, BMAA0186 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q62E64, UniProt: A0A0H2WBM4*PLUS, benzoate 1,2-dioxygenase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15.0000% Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97822,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978221
30.979011
ReflectionResolution: 1.9→29.476 Å / Num. obs: 14285 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 26.262 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allMean I/σ(I) obsNum. measured allNum. unique allRrim(I) allRsym value% possible all
1.9-1.955.30.50931.4542010220.5680.509100
1.95-25.30.4553.31.752619990.5070.455100
2-2.065.30.3374.52.351899740.3750.337100
2.06-2.125.20.285.42.649299490.3130.28100
2.12-2.195.30.2256.63.449239270.250.225100
2.19-2.275.20.227.43.247269150.2460.22100
2.27-2.365.30.1688.94.445508640.1880.168100
2.36-2.455.20.1410.25.343218300.1570.14100
2.45-2.565.20.11812.26.342448150.1320.118100
2.56-2.695.20.10114.37.240537850.1130.101100
2.69-2.835.20.082178.537777270.0920.082100
2.83-35.20.07419.5936407030.0830.07499.6
3-3.215.20.06323.41033806550.070.06399.6
3.21-3.475.20.05127.112.632856340.0570.05199.5
3.47-3.850.04430.913.628575700.0490.04499.4
3.8-4.255.10.04433.310.826875270.0490.04498.7
4.25-4.915.10.0423314.323734690.0460.04298.6
4.91-6.014.90.03930.815.619474010.0430.03997.5
6.01-8.54.80.04229.613.615413240.0470.04296.4
8.5-29.4840.0427.713.47861950.0460.0491

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.476 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.624 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. ACETATE (ACT) IS PRESENT IN CRYSTALLIZATION CONDITION. 5. RAMACHANDRAN OUTLIER TYR119 IS LOCATED IN A DISORDERED REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 717 5 %RANDOM
Rwork0.186 ---
obs0.188 14242 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.57 Å2 / Biso mean: 30.839 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 4 139 1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221315
X-RAY DIFFRACTIONr_bond_other_d0.0020.02907
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9271786
X-RAY DIFFRACTIONr_angle_other_deg0.91132166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70721.88469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9915216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9071515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_nbd_refined0.1990.2220
X-RAY DIFFRACTIONr_nbd_other0.2190.2914
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2614
X-RAY DIFFRACTIONr_nbtor_other0.0840.2746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.227
X-RAY DIFFRACTIONr_mcbond_it2.0953783
X-RAY DIFFRACTIONr_mcbond_other0.5663306
X-RAY DIFFRACTIONr_mcangle_it3.09951242
X-RAY DIFFRACTIONr_scbond_it4.9668621
X-RAY DIFFRACTIONr_scangle_it5.89211541
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 52 -
Rwork0.24 969 -
all-1021 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.5689 Å / Origin y: 14.8213 Å / Origin z: 20.3377 Å
111213212223313233
T-0.0395 Å2-0.0066 Å20.0008 Å2--0.0208 Å2-0.0504 Å2---0.0312 Å2
L1.2153 °20.3644 °20.3614 °2-1.2226 °20.0092 °2--0.1163 °2
S-0.0735 Å °-0.016 Å °0.0583 Å °-0.0509 Å °-0.0307 Å °0.2498 Å °-0.0167 Å °-0.051 Å °0.1042 Å °

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