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- PDB-2gvk: Crystal structure of a dye-decolorizing peroxidase (DyP) from Bac... -

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Basic information

Entry
Database: PDB / ID: 2gvk
TitleCrystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution
ComponentsHeme peroxidase
KeywordsOXIDOREDUCTASE / pc04261d / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI / Heme peroxidase
Function / homology
Function and homology information


peroxidase activity / heme binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
ACETIC ACID / Unknown ligand / : / Peroxidase family protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
Authors: Zubieta, C. / Krishna, S.S. / Kapoor, M. / Kozbial, P. / McMullan, D. / Axelrod, H.L. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / ...Authors: Zubieta, C. / Krishna, S.S. / Kapoor, M. / Kozbial, P. / McMullan, D. / Axelrod, H.L. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kumar, A. / Marciano, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Reyes, R. / Rife, C.L. / Schimmel, P. / van den Bedem, H. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr1_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,19613
Polymers35,6361
Non-polymers56012
Water5,747319
1
A: Heme peroxidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)217,17678
Polymers213,8176
Non-polymers3,35972
Water1086
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area29340 Å2
ΔGint-216 kcal/mol
Surface area62540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.090, 109.090, 122.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Heme peroxidase


Mass: 35636.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1219 / Production host: Escherichia coli (E. coli) / References: GenBank: 29338526, UniProt: Q8A8E8*PLUS

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Non-polymers , 6 types, 331 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 0.2M Li2SO4, 2.5M NaCl, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97920, 0.97903, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979031
30.918371
ReflectionResolution: 1.6→29.05 Å / Num. obs: 56989 / % possible obs: 99.7 % / Redundancy: 14.16 % / Biso Wilson estimate: 24.466 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.6690.40.8842.3707131018198.7
1.66-1.72940.7173.1688509135
1.72-1.895.20.56747972010539
1.8-1.996.40.415.38256510884
1.9-2.0297.50.2767.78002510522
2.02-2.1798.40.19310.37745110151
2.17-2.39990.12614.78225810740
2.39-2.7399.50.09418.48142710609
2.7399.80.06268247310787

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.838 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072
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 INCORPOR DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE M ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPOR DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE M RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING DUE TO PARTIAL S-MET INCORPORATION. 3. THE ELECTRON DENISTY FOR RESIDUES 246-247 WAS DIFFICULT TO INTERPRET AND MAY BE POORLY MODELLED. 4. UNL (UNKNOWN LIGAND) WAS MODELLED INTO EXTRA DENSITY NEAR RESIDUES 247-249. THIS REGION MAY DENOTE THE PROTEIN ACTIVE SITE. 5. ADDITIONAL DENSITY NEAR UNL WAS INTERPRETED TO BE WATER. 6. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. THE MEAN B VALUE INCLUDING THE INDIVIDUAL AND TLS COMPONENTS IS 20.7 A**2.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2886 5.1 %RANDOM
Rwork0.164 ---
all0.165 ---
obs0.16542 56989 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 37 319 2744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222660
X-RAY DIFFRACTIONr_bond_other_d0.0010.022374
X-RAY DIFFRACTIONr_angle_refined_deg0.9571.9523637
X-RAY DIFFRACTIONr_angle_other_deg0.57135552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63324.436133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5441515
X-RAY DIFFRACTIONr_chiral_restr0.060.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
X-RAY DIFFRACTIONr_nbd_refined0.220.2536
X-RAY DIFFRACTIONr_nbd_other0.2020.22345
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21302
X-RAY DIFFRACTIONr_nbtor_other0.0890.21435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1430.21
X-RAY DIFFRACTIONr_metal_ion_refined0.050.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.217
X-RAY DIFFRACTIONr_mcbond_it0.40811629
X-RAY DIFFRACTIONr_mcbond_other0.0251668
X-RAY DIFFRACTIONr_mcangle_it1.01732652
X-RAY DIFFRACTIONr_scbond_it2.63451051
X-RAY DIFFRACTIONr_scangle_it4.1388955
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 218 -
Rwork0.243 3916 -
obs-4134 99.86 %
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)
110.1592-0.4698-0.17436.91143.481410.9094-0.1460.0416-0.52950.2411-0.07960.21420.5801-0.23840.22550.0667-0.00360.00580.0220.00510.012455.73744.7836.313
20.80270.1766-0.13310.2684-0.10450.5636-0.00560.06920.0542-0.01330.02530.0069-0.05040.0015-0.01970.0362-0.00120.00490.00630.0107-0.020751.76754.25915.208
30.7203-0.29-0.10210.28970.08410.43410.02440.08880.0047-0.01650.00980.0332-0.0197-0.145-0.03430.04270.0033-0.00740.04940.0275-0.003339.92856.94513.344
420.01398.72374.489311.10952.297310.18920.01681.0173-0.7085-0.40490.3467-0.60250.0050.5338-0.36350.04280.00430.02950.0857-0.0184-0.03467.65252.3931.449
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
118 - 209 - 21
2221 - 22222 - 223
33223 - 308224 - 309
44309 - 316310 - 317

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