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- PDB-3e5d: Crystal structure of a putative glyoxalase i (lmof2365_0426) from... -

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Basic information

Entry
Database: PDB / ID: 3e5d
TitleCrystal structure of a putative glyoxalase i (lmof2365_0426) from listeria monocytogenes str. 4b f2365 at 2.70 A resolution
ComponentsPutative Glyoxalase I
KeywordsLYASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / Unknown ligand / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Glyoxalase I (YP_013033.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: 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
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Glyoxalase I


Theoretical massNumber of molelcules
Total (without water)14,5022
Polymers14,5021
Non-polymers01
Water362
1
A: Putative Glyoxalase I

A: Putative Glyoxalase I


Theoretical massNumber of molelcules
Total (without water)29,0054
Polymers29,0052
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_655-x+1,-y+1/2,z1
Buried area4980 Å2
ΔGint-35 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.590, 123.590, 123.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
DetailsAUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.

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Components

#1: Protein Putative Glyoxalase I


Mass: 14502.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria)
Gene: LMOf2365_0426 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q723Q1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details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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: 5.42 Å3/Da / Density % sol: 77.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M sodium citrate, 0.15M sodium chloride, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→29.136 Å / Num. obs: 8775 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 103.91 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.7-2.80.9912.2139821700198.8
2.8-2.910.6053.61440116561100
2.91-3.040.3516.11421616331100
3.04-3.20.19210.51471916901100
3.2-3.40.10617.61458716771100
3.4-3.660.07523.2143291652199.9
3.66-4.030.051331450016831100
4.03-4.60.0439.4143951669199.9
4.6-5.770.036421418616441100
5.77-29.1360.03444.1145831722198.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.136 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 13.998 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.189
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN TENTATIVELY MODELED AT WHAT APPEARS TO BE THE PUTATIVE ACTIVE SITE(S) SURROUNDED BY RESIDUES HIS5, PHE39, GLU53, ARG57, HIS73, ASP107, GLU111 AND GLU123.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 416 4.7 %RANDOM
Rwork0.172 ---
obs0.173 8766 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.474 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 9 2 1007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221017
X-RAY DIFFRACTIONr_bond_other_d0.0010.02666
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9351378
X-RAY DIFFRACTIONr_angle_other_deg0.95931618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0315125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.22424.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37715168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.148155
X-RAY DIFFRACTIONr_chiral_restr0.0950.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2180.2179
X-RAY DIFFRACTIONr_nbd_other0.1850.2647
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2494
X-RAY DIFFRACTIONr_nbtor_other0.0850.2520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3760.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.23
X-RAY DIFFRACTIONr_mcbond_it1.3733681
X-RAY DIFFRACTIONr_mcbond_other0.2433261
X-RAY DIFFRACTIONr_mcangle_it2.1345995
X-RAY DIFFRACTIONr_scbond_it3.9738449
X-RAY DIFFRACTIONr_scangle_it5.12711383
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.504 35 -
Rwork0.427 607 -
all-642 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 59.8985 Å / Origin y: 22.1081 Å / Origin z: 31.8695 Å
111213212223313233
T0.0249 Å2-0.0146 Å20.0023 Å2-0.0818 Å2-0.0445 Å2---0.0103 Å2
L3.7815 °2-1.3178 °20.6147 °2-3.0936 °20.1987 °2--1.2344 °2
S0.111 Å °0.4266 Å °-0.3703 Å °-0.2088 Å °-0.0806 Å °0.2793 Å °0.1659 Å °-0.0032 Å °-0.0303 Å °

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