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- PDB-3iuz: Crystal structure of Putative glyoxalase superfamily protein (YP_... -

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Entry
Database: PDB / ID: 3iuz
TitleCrystal structure of Putative glyoxalase superfamily protein (YP_299723.1) from RALSTONIA EUTROPHA JMP134 at 1.90 A resolution
ComponentsPutative glyoxalase superfamily protein
KeywordsLYASE / YP_299723.1 / Putative glyoxalase superfamily protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


2-oxoadipate dioxygenase/decarboxylase / dioxygenase activity
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 - #50 / Domain of unknown function DUF1338 / 2-oxoadipate dioxygenase/decarboxylase / DUF1338 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / 2-oxoadipate dioxygenase/decarboxylase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative glyoxalase superfamily protein (YP_299723.1) from RALSTONIA EUTROPHA JMP134 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _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: Putative glyoxalase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5207
Polymers37,4871
Non-polymers1,0336
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.069, 114.069, 133.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

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Components

#1: Protein Putative glyoxalase superfamily protein


Mass: 37487.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_B5534, YP_299723.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46PQ5
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. 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. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40.0000% polyethylene glycol 600, 0.1M sodium citrate pH 5.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97860,0.97806
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97861
30.978061
ReflectionResolution: 1.9→28.904 Å / Num. obs: 34930 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 21.874 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.957.40.9860.81880425390.986100
1.95-27.40.78111848324910.781100
2-2.067.40.6061.31781923960.606100
2.06-2.127.40.5131.51743223470.513100
2.12-2.197.40.421.81703122940.42100
2.19-2.277.50.3552.11643122050.355100
2.27-2.367.40.3042.51573521130.304100
2.36-2.457.40.2682.81536020720.268100
2.45-2.567.50.2133.61474919750.213100
2.56-2.697.40.184.21406118960.18100
2.69-2.837.40.1574.81337918040.157100
2.83-37.40.1335.51264217100.133100
3-3.217.40.1076.61182015980.107100
3.21-3.477.30.0864.11108215100.086100
3.47-3.87.30.0669.81024213950.066100
3.8-4.257.30.05710.5923212710.057100
4.25-4.917.20.06210.3820911340.062100
4.91-6.017.10.078.468869670.07100
6.01-8.570.04912.453137620.049100
8.5-28.916.30.04811.228444510.04897.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.904 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.507 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.118
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 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. POLY ETHYLENE GLYCOL FRAGMENTS (PGE, P6G) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1752 5 %RANDOM
Rwork0.167 ---
obs0.169 34930 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.29 Å2 / Biso mean: 22.177 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 66 291 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222646
X-RAY DIFFRACTIONr_bond_other_d0.0010.021855
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9743579
X-RAY DIFFRACTIONr_angle_other_deg0.90534474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03122.713129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815.061413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.461530
X-RAY DIFFRACTIONr_chiral_restr0.090.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_mcbond_it0.9461.51615
X-RAY DIFFRACTIONr_mcbond_other0.281.5666
X-RAY DIFFRACTIONr_mcangle_it1.62522590
X-RAY DIFFRACTIONr_scbond_it2.47731031
X-RAY DIFFRACTIONr_scangle_it3.854.5978
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 136 -
Rwork0.237 2397 -
all-2533 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 22.091 Å / Origin y: 49.7009 Å / Origin z: 17.5344 Å
111213212223313233
T0.0018 Å20.0048 Å20.0043 Å2-0.0294 Å20.0191 Å2--0.0141 Å2
L0.2447 °20.0711 °20.0315 °2-0.414 °2-0.1715 °2--0.4841 °2
S0.0016 Å °-0.0255 Å °-0.0023 Å °0.0247 Å °0.031 Å °0.0417 Å °-0.0141 Å °-0.0321 Å °-0.0327 Å °

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