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- PDB-4z6w: Structure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase... -

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Basic information

Entry
Database: PDB / ID: 4z6w
TitleStructure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.57 Ang resolution
ComponentsHomoprotocatechuate 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / 2-His-1-carboxylate facial triad / oxygen activation / acid-base catalysis
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
homoprotocatechuate 2,3-dioxygenase fold / homoprotocatechuate 2,3-dioxygenase domains / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain ...homoprotocatechuate 2,3-dioxygenase fold / homoprotocatechuate 2,3-dioxygenase domains / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Few Secondary Structures / Irregular / Roll / Alpha Beta
Similarity search - Domain/homology
4-NITROCATECHOL / : / DI(HYDROXYETHYL)ETHER / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsKovaleva, E.G. / Lipscomb, J.D.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H001905/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 24689 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200.
Authors: Kovaleva, E.G. / Rogers, M.S. / Lipscomb, J.D.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_alt_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_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoprotocatechuate 2,3-dioxygenase
B: Homoprotocatechuate 2,3-dioxygenase
C: Homoprotocatechuate 2,3-dioxygenase
D: Homoprotocatechuate 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,53923
Polymers166,9254
Non-polymers2,61419
Water30,8421712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19430 Å2
ΔGint-105 kcal/mol
Surface area43790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.469, 150.646, 95.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21D-919-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Homoprotocatechuate 2,3-dioxygenase


Mass: 41731.277 Da / Num. of mol.: 4 / Mutation: H200N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Plasmid: pYZW204 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: Q45135

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Non-polymers , 7 types, 1731 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO4
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1712 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG6000, 0.1M calcium acetate, 0.1M MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.57→48 Å / Num. all: 218224 / Num. obs: 218224 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Rsym value: 0.09 / Net I/av σ(I): 6.3 / Net I/σ(I): 12.6 / Num. measured all: 1452866
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.57-1.655.80.8131177657307070.3670.8132.295.3
1.65-1.766.90.5691.4204240296200.2320.5693.597.2
1.76-1.886.90.3562.2194259281280.1450.3565.397.9
1.88-2.036.90.2153.6181143262840.0880.2158.498.3
2.03-2.226.80.1395.5166472243390.0570.13912.398.7
2.22-2.486.80.17.4150872221640.0410.11699
2.48-2.876.80.0759.3133224196350.0310.07520.599.3
2.87-3.516.70.05611.1112165167620.0230.05627.799.6
3.51-4.966.50.04712.885077131120.020.04734.299.8
4.96-45.7336.40.04412.74775774730.0190.04432.999.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJT

3ojt


Resolution: 1.57→45.73 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.1291 / FOM work R set: 0.8953 / SU B: 2.826 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0665 / SU Rfree: 0.0675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1629 10854 5 %RANDOM
Rwork0.1373 ---
obs0.1386 207317 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 76.52 Å2 / Biso mean: 20.802 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.57→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11515 0 161 1721 13397
Biso mean--27.47 32.13 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211262
X-RAY DIFFRACTIONr_angle_refined_deg1.531.95216865
X-RAY DIFFRACTIONr_angle_other_deg0.84325917
X-RAY DIFFRACTIONr_chiral_restr0.10.21742
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023069
X-RAY DIFFRACTIONr_mcbond_it0.9871.4985940
X-RAY DIFFRACTIONr_mcbond_other0.9831.4985939
X-RAY DIFFRACTIONr_mcangle_it1.4232.5217502
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 715 -
Rwork0.263 14638 -
all-15353 -
obs--94.12 %
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)
10.5454-0.20670.03310.3894-0.01180.2224-0.00960.08930.2586-0.046-0.0466-0.1368-0.04840.03890.05620.0199-0.0074-0.00760.07870.06180.150812.40153.0976.181
20.474-0.0357-0.16090.26420.03550.3614-0.01050.17850.0099-0.05650.0078-0.04620.0173-0.11310.00270.027-0.01140.01130.15320.01650.01312.04922.173-7.384
30.50130.0206-0.03650.42430.07310.4257-0.0101-0.11080.10220.1011-0.01370.0230.0072-0.05520.02380.03230.00870.00070.103-0.02640.0237-2.83130.63938.694
40.59090.06880.0490.49090.0850.32390.0009-0.0789-0.07030.09680.0082-0.1250.07640.0423-0.00920.03440.0188-0.02270.07620.01070.040624.93112.5631.037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 358
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B4 - 362
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C4 - 356
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D4 - 362
8X-RAY DIFFRACTION4D401

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