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- PDB-3c5m: Crystal structure of oligogalacturonate lyase (VPA0088) from Vibr... -

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Basic information

Entry
Database: PDB / ID: 3c5m
TitleCrystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199
ComponentsOligogalacturonate lyase
KeywordsLYASE / 7 blade-shaped beta-propeller / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


oligogalacturonide lyase activity / pectin catabolic process / metal ion binding
Similarity search - Function
Oligogalacturonate lyase domain / Oligogalacturonate lyase / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Oligogalacturonate lyase
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Baran, M.C. / Acton, T.B. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus.
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / 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_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.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

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Assembly

Deposited unit
A: Oligogalacturonate lyase
B: Oligogalacturonate lyase
C: Oligogalacturonate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2276
Polymers137,0623
Non-polymers1653
Water3,765209
1
A: Oligogalacturonate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7422
Polymers45,6871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oligogalacturonate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7422
Polymers45,6871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Oligogalacturonate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7422
Polymers45,6871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.233, 115.233, 209.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Oligogalacturonate lyase


Mass: 45687.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA0088 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q87K10
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT ELECTRON DENSITY CLEARLY SHOWS THAT THE RESIDUE AT THE SEQUENCE POSITION 31 IS ...AUTHORS STATE THAT ELECTRON DENSITY CLEARLY SHOWS THAT THE RESIDUE AT THE SEQUENCE POSITION 31 IS NOT VALINE. THE ILE SIDE CHAIN HAS BEEN MODELED ACCORDING TO THE ELECTRON DENSITY AT SEQUENCE POSITION 31.

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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: 2.94 Å3/Da / Density % sol: 58.12 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM MES pH 6.5, 20% PEG 3350, 100 mM Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 94903 / Num. obs: 94903 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.105 / Net I/σ(I): 18.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.297

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 242133.24 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.277 8428 9.8 %RANDOM
Rwork0.234 ---
obs0.234 86115 89.8 %-
all-95896 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.171 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 50.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.16 Å20 Å20 Å2
2--8.16 Å20 Å2
3----16.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 3 209 9292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 558 10.2 %
Rwork0.338 4895 -
obs--57 %

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