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- PDB-1u9c: Crystallographic structure of APC35852 -

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Basic information

Entry
Database: PDB / ID: 1u9c
TitleCrystallographic structure of APC35852
ComponentsAPC35852
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / Parkinson's disease / chaperone / cysteine protease / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / cytoplasm
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypothetical conserved protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBorek, D. / Chen, Y. / Shao, D. / Collart, F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structural analysis of DJI superfamily
Authors: Borek, D. / Chen, Y. / Shao, D. / Collart, F. / Joachimiak, A. / Otwinowski, Z.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 19, 2014Group: Non-polymer description
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APC35852


Theoretical massNumber of molelcules
Total (without water)24,7411
Polymers24,7411
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.183, 66.183, 53.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein APC35852


Mass: 24740.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KWF3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2M magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9797 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 12, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SAGITALLY FOCUSED SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 47601 / Num. obs: 49550 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.236 / Net I/σ(I): 53.7
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3715 / % possible all: 72.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RW7

1rw7
PDB Unreleased entry


Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.791 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19729 2484 5 %RANDOM
Rwork0.17215 ---
all0.1734 49550 --
obs0.1734 46862 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 0 187 1910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211763
X-RAY DIFFRACTIONr_bond_other_d0.0010.021574
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9392392
X-RAY DIFFRACTIONr_angle_other_deg0.89633668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25624.40584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30615292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391511
X-RAY DIFFRACTIONr_chiral_restr0.2910.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.2370.2356
X-RAY DIFFRACTIONr_nbd_other0.1810.21601
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2886
X-RAY DIFFRACTIONr_nbtor_other0.0860.21041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.218
X-RAY DIFFRACTIONr_symmetry_hbond_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.4671.51386
X-RAY DIFFRACTIONr_mcbond_other0.3741.5453
X-RAY DIFFRACTIONr_mcangle_it1.75321771
X-RAY DIFFRACTIONr_scbond_it2.8393758
X-RAY DIFFRACTIONr_scangle_it3.794.5621
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 125 -
Rwork0.232 2573 -
obs-3715 71.93 %
Refinement TLS params.Method: refined / Origin x: 25.224 Å / Origin y: 10.158 Å / Origin z: 40.107 Å
111213212223313233
T-0.0615 Å2-0.0004 Å20.0238 Å2--0.0196 Å20.0231 Å2---0.0439 Å2
L2.7258 °2-0.801 °2-0.6458 °2-1.0132 °20.2941 °2--1.1619 °2
S0.1255 Å °0.0243 Å °0.3659 Å °-0.0364 Å °0.0469 Å °-0.1367 Å °-0.113 Å °-0.0538 Å °-0.1724 Å °

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