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- PDB-3b59: Crystal structure of the Mn(II)-bound glyoxalase from Novosphingo... -

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Basic information

Entry
Database: PDB / ID: 3b59
TitleCrystal structure of the Mn(II)-bound glyoxalase from Novosphingobium aromaticivorans
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsLYASE / 11004z / Glyoxalase / NYSGXRC / PSI-2 / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / Dioxygenase
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
: / Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å
AuthorsMadegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the Mn(II)-bound glyoxalase from Novosphingobium aromaticivorans.
Authors: Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
C: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase
E: Glyoxalase/bleomycin resistance protein/dioxygenase
F: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,77112
Polymers207,4416
Non-polymers3306
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.997, 168.348, 202.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 34573.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_0713 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2GAG3
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 58.76 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 9, 2007 / Details: SGX-CAT
RadiationMonochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.53→31.69 Å / Num. all: 160103 / Num. obs: 160103 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 19.9
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.8 / Num. unique all: 24096 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.53→29.57 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 351101.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of ...Details: The Friedel pairs were used in phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 7716 5 %RANDOM
Rwork0.218 ---
obs0.218 154584 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.9299 Å2 / ksol: 0.369814 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.81 Å20 Å20 Å2
2--8.01 Å20 Å2
3----1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.53→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13998 0 6 232 14236
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.53→2.69 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 1195 4.9 %
Rwork0.312 23146 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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