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- PDB-4dgq: Crystal structure of Non-heme chloroperoxidase from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 4dgq
TitleCrystal structure of Non-heme chloroperoxidase from Burkholderia cenocepacia
ComponentsNon-heme chloroperoxidase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


chloride peroxidase / chloride peroxidase activity
Similarity search - Function
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
Non-heme chloroperoxidase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 1.85 Å
AuthorsGardberg, A.S. / Edwards, T.E. / Abendroth, J.A. / Staker, B. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Non-heme chloroperoxidase from Burkholderia cenocepacia
Authors: Gardberg, A.S. / Edwards, T.E. / Abendroth, J.A. / Staker, B. / Stewart, L.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Non-heme chloroperoxidase
B: Non-heme chloroperoxidase
C: Non-heme chloroperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9276
Polymers91,7413
Non-polymers1863
Water15,457858
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-24 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.770, 111.850, 80.210
Angle α, β, γ (deg.)90.000, 111.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-heme chloroperoxidase


Mass: 30580.225 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: cpo, BceJ2315_07640, BCAL0771 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EA96, chloride peroxidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Internal tracking number 228044H10. Wizard III/IV screen condition H10: 30% 2-propanol, 30% PEG3350, 0.1 M Tris, pH 8.5. BuceA00095hA1 PS01264 at 21.88mg/ml in a stabilizing buffer of 25 mM ...Details: Internal tracking number 228044H10. Wizard III/IV screen condition H10: 30% 2-propanol, 30% PEG3350, 0.1 M Tris, pH 8.5. BuceA00095hA1 PS01264 at 21.88mg/ml in a stabilizing buffer of 25 mM HEPES, pH 7.0, 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 84726 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 19.591 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 20.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.93.20.5042.720063618698.1
1.9-1.950.4273.927104604199.6
1.95-2.010.3625.738112593599.9
2.01-2.070.3057.242445575899.9
2.07-2.140.2469.547591556099.9
2.14-2.210.21112.454955539499.9
2.21-2.290.18714.958551526199.8
2.29-2.390.16117.360945501499.9
2.39-2.490.1571967186482799.8
2.49-2.620.14520.768652459999.9
2.62-2.760.12522.866392441899.8
2.76-2.930.10925.661906410899.9
2.93-3.130.09329.359359391399.9
3.13-3.380.07835.455656365999.7
3.38-3.70.06446.2502503320100
3.7-4.140.05653.545808302599.5
4.14-4.780.05157.140374268599.7
4.78-5.850.05448.634631226899.9
5.85-8.270.05842.426867176299.7
8.27-500.03468.81420599398

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 1zoi

1zoi


Resolution: 1.85→39.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.61 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 4223 5 %RANDOM
Rwork0.135 ---
obs0.136 84695 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.905 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 12 858 7264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026639
X-RAY DIFFRACTIONr_bond_other_d0.0020.024350
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9199044
X-RAY DIFFRACTIONr_angle_other_deg0.97310566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27823.742310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40415974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1211531
X-RAY DIFFRACTIONr_chiral_restr0.1060.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021427
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 276 -
Rwork0.214 5786 -
all-6062 -
obs--98.12 %
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)
11.1876-0.3997-1.42920.99680.81992.65050.04940.13990.1418-0.18890.03880.157-0.0904-0.113-0.08820.04350.005-0.03550.06960.03550.0656-22.5371.528-26.299
20.32260.10380.04190.3540.09650.38320.0330.0429-0.016-0.0251-0.03130.0740.0334-0.0563-0.00170.0203-0.0029-0.02210.0322-0.0090.0365-22.918-10.859-18.465
30.51130.10620.03070.4585-0.03630.33870.0130.0183-0.0501-0.0076-0.00750.01290.0798-0.0001-0.00550.026-0.0039-0.01180.0092-0.00290.0263-15.136-17.498-16.31
42.17371.2616-0.62892.2385-1.30871.2311-0.03710.12640.0989-0.02590.04120.1591-0.055-0.1995-0.00410.02610.0177-0.01250.0883-0.02070.0738-24.32311.647-4.11
50.37540.2451-0.05850.33310.10370.29910.0251-0.0190.04690.0206-0.01420.0336-0.0427-0.0259-0.01090.02460.00090.00980.013-0.00710.0369-13.55115.8234.974
60.58880.0079-0.17350.50080.19120.56450.012-0.07870.01840.05680.008-0.02320.00730.0822-0.01990.0125-0.0029-0.00350.0189-0.0060.0088-6.1569.359.318
72.14111.35351.02332.45071.19181.49890.07170.06580.1714-0.0358-0.03020.1813-0.1903-0.0981-0.04150.09330.03480.0260.03530.03240.0833-9.17821.881-20.881
80.26710.0644-0.29040.2290.01450.51250.02510.06010.0693-0.040.0090.0192-0.07180.012-0.03410.0413-0.00680.00420.05230.0350.02891.15914.908-28.844
90.38660.0534-0.18260.3472-0.14880.65840.01770.0435-0.0022-0.0475-0.0038-0.0597-0.03440.1004-0.0140.0143-0.01040.00980.05350.00790.02299.75810.214-25.164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 149
3X-RAY DIFFRACTION3A150 - 276
4X-RAY DIFFRACTION4B1 - 23
5X-RAY DIFFRACTION5B24 - 149
6X-RAY DIFFRACTION6B150 - 276
7X-RAY DIFFRACTION7C1 - 23
8X-RAY DIFFRACTION8C24 - 149
9X-RAY DIFFRACTION9C150 - 276

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