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- PDB-1w8g: CRYSTAL STRUCTURE OF E. COLI K-12 YGGS -

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Basic information

Entry
Database: PDB / ID: 1w8g
TitleCRYSTAL STRUCTURE OF E. COLI K-12 YGGS
ComponentsHYPOTHETICAL UPF0001 PROTEIN YGGS
KeywordsPLP-BINDING PROTEIN / STRUCTURAL GENOMICS / HYPOTHETICAL PROTEIN / PUTATIVE ENZYME WITH PLP-BINDING DOMAIN
Function / homology
Function and homology information


pyridoxal phosphate binding / cytosol
Similarity search - Function
Uncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ISOCITRIC ACID / PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate homeostasis protein / Pyridoxal phosphate homeostasis protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSulzenbacher, G. / Gruez, A. / Spinelli, S. / Roig-Zamboni, V. / Pagot, F. / Bignon, C. / Vincentelli, R. / Cambillau, C.
CitationJournal: To be Published
Title: Crystal Structure of E. Coli K-12 Yggs
Authors: Sulzenbacher, G. / Gruez, A. / Spinelli, S. / Roig-Zamboni, V. / Pagot, F. / Bignon, C. / Vincentelli, R. / Cambillau, C.
History
DepositionSep 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL UPF0001 PROTEIN YGGS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2603
Polymers25,8201
Non-polymers4392
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.017, 124.017, 83.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2029-

HOH

21A-2067-

HOH

31A-2068-

HOH

41A-2083-

HOH

51A-2137-

HOH

61A-2181-

HOH

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Components

#1: Protein HYPOTHETICAL UPF0001 PROTEIN YGGS / YGGS


Mass: 25820.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PLP-BINDING DOMAIN, COMPLEX WITH PLP / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52054, UniProt: P67080*PLUS
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6
Details: 20% PEG 4000, 16% ISOPROPANOL, 0.1 M NA-CITRATE BUFFER PH 6, 5% SODIUM DEXTRANE SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→39 Å / Num. obs: 22295 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 25.32 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 34.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B54

1b54


Resolution: 2→39 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.364 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TOTAL B VALUES (TLS COMPONENT + RESIDUAL) ARE GIVEN FOR EACH ATOM
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1222 5.5 %RANDOM
Rwork0.161 ---
obs0.163 21064 100 %-
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: 21.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 28 274 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021754
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9752525
X-RAY DIFFRACTIONr_angle_other_deg0.77434061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17923.03489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15315329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1071522
X-RAY DIFFRACTIONr_chiral_restr0.0620.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined0.2080.2344
X-RAY DIFFRACTIONr_nbd_other0.1860.21716
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2894
X-RAY DIFFRACTIONr_nbtor_other0.0820.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8191.51498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87621846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5573796
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3374.5675
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.196 71
Rwork0.172 1504
Refinement TLS params.Method: refined / Origin x: 82.0717 Å / Origin y: 6.7642 Å / Origin z: 8.0175 Å
111213212223313233
T-0.0308 Å2-0.0103 Å20.0168 Å2--0.0408 Å2-0.0065 Å2---0.0327 Å2
L0.9542 °20.1585 °20.1848 °2-0.7441 °2-0.2411 °2--1.0584 °2
S0.0023 Å °-0.0251 Å °0.0009 Å °0.034 Å °0.0085 Å °0.0134 Å °0.0077 Å °-0.0104 Å °-0.0108 Å °

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