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- PDB-4nvs: Crystal Structure of the Q18CP6_CLOD6 protein from glyoxalase fam... -

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Basic information

Entry
Database: PDB / ID: 4nvs
TitleCrystal Structure of the Q18CP6_CLOD6 protein from glyoxalase family. Northeast Structural Genomics Consortium Target CfR3
ComponentsPutative enzyme, glyoxalase family
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / CfR3 / putative glyoxalase / PF12681 / PF00903
Function / homology
Function and homology information


Glyoxalase-like domain / Glyoxalase-like domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Enzyme, glyoxalase family
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.385 Å
AuthorsVorobiev, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Q18CP6_CLOD6 protein from glyoxalase family.
Authors: Vorobiev, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative enzyme, glyoxalase family
B: Putative enzyme, glyoxalase family


Theoretical massNumber of molelcules
Total (without water)38,8292
Polymers38,8292
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-26 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.388, 52.168, 135.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative enzyme, glyoxalase family


Mass: 19414.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_01590 / Plasmid: CfR3-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q18CP6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 5.8
Details: 27% PEG 3350, 5% 1-ethyl-3-methylimidazolium chloride, 0.1 M MES pH 5.8, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 27440 / Num. obs: 27413 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 42.13 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2715 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.385→28.176 Å / Occupancy max: 1 / Occupancy min: 0.73 / SU ML: 0.91 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1373 5.06 %RANDOM
Rwork0.223 ---
obs0.226 27121 98.44 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.245 Å2 / ksol: 0.287 e/Å3
Displacement parametersBiso max: 155.05 Å2 / Biso mean: 61.755 Å2 / Biso min: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1--6.265 Å20 Å2-0 Å2
2--37.188 Å2-0 Å2
3----30.924 Å2
Refinement stepCycle: LAST / Resolution: 2.385→28.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 0 103 2676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092617
X-RAY DIFFRACTIONf_angle_d1.363523
X-RAY DIFFRACTIONf_chiral_restr0.085393
X-RAY DIFFRACTIONf_plane_restr0.005449
X-RAY DIFFRACTIONf_dihedral_angle_d17.572969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.385-2.470.4621400.3522409254993
2.47-2.5690.3841450.33626012746100
2.569-2.6860.4221550.3492581273699
2.686-2.8270.421150.28526312746100
2.827-3.0040.3411520.2572582273499
3.004-3.2360.3071500.2442569271999
3.236-3.5610.3021340.2292598273299
3.561-4.0750.2291320.2012562269498
4.075-5.1290.2361250.1612599272499
5.129-28.1780.2161250.1952616274199
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)
11.0943-0.2850.32710.2383-0.29551.6378-0.0472-0.0125-0.01880.04010.05670.0432-0.1923-0.0989-00.1657-0.02860.00930.12690.02140.17318.522219.088951.4731
20.6624-0.43280.39780.59-0.26651.64490.16810.128-0.0721-0.0729-0.12110.02490.14940.142800.2642-0.0744-0.00090.3210.00190.286231.20845.779150.4852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 156
2X-RAY DIFFRACTION2chain BB1 - 157

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