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- PDB-1yac: THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE YCAC GENE PRODUCT FROM ... -

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Basic information

Entry
Database: PDB / ID: 1yac
TitleTHE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE YCAC GENE PRODUCT FROM ESCHERICHIA COLI REVEALS AN OCTAMERIC HYDROLASE OF UNKNOWN SPECIFICITY
ComponentsYCAC GENE PRODUCT
KeywordsUNKNOWN BACTERIAL HYDROLASE / THREE LAYER ALPHA-BETA-ALPHA SANDWICH TOPOLOGY / ENTB HOMOLOG / CSHASE HOMOLOG
Function / homology
Function and homology information


Lyases / hydrolase activity / lyase activity / identical protein binding / membrane / cytosol
Similarity search - Function
: / : / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable hydrolase YcaC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsColovos, C. / Cascio, D. / Yeates, T.O.
CitationJournal: Structure / Year: 1998
Title: The 1.8 A crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity.
Authors: Colovos, C. / Cascio, D. / Yeates, T.O.
History
DepositionJul 29, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YCAC GENE PRODUCT
B: YCAC GENE PRODUCT


Theoretical massNumber of molelcules
Total (without water)45,9562
Polymers45,9562
Non-polymers00
Water4,846269
1
A: YCAC GENE PRODUCT
B: YCAC GENE PRODUCT

A: YCAC GENE PRODUCT
B: YCAC GENE PRODUCT

A: YCAC GENE PRODUCT
B: YCAC GENE PRODUCT

A: YCAC GENE PRODUCT
B: YCAC GENE PRODUCT


Theoretical massNumber of molelcules
Total (without water)183,8258
Polymers183,8258
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area34520 Å2
ΔGint-133 kcal/mol
Surface area47470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.898, 91.898, 113.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

21B-265-

HOH

31B-313-

HOH

41B-314-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.151263, 0.988474, -0.00626), (0.988483, 0.151287, 0.00357), (0.004476, -0.005648, -0.999974)
Vector: 53.364, -45.644, 55.334)

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Components

#1: Protein YCAC GENE PRODUCT / YCACGP


Mass: 22978.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YCAC / References: UniProt: P21367
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.57 Å3/Da / Density % sol: 41 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.4 Mammonium sulfate1reservoir
2100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: ADSC / Detector: CCD / Date: Jul 9, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 45552 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.39 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.64
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.56 / % possible all: 97.6
Reflection
*PLUS
Num. obs: 45076 / % possible obs: 98.8 % / Num. measured all: 308775 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 95.6 % / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→8 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4376 10 %RANDOM
Rwork0.1748 ---
obs0.1748 45522 99.7 %-
Displacement parametersBiso mean: 14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 0 269 3435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.618
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2351 554 12.6 %
Rwork0.2187 4857 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CISPEP.INP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.2187

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