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- PDB-1rc6: Crystal structure of protein Ylba from E. coli, Pfam DUF861 -

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Basic information

Entry
Database: PDB / ID: 1rc6
TitleCrystal structure of protein Ylba from E. coli, Pfam DUF861
ComponentsHypothetical protein ylbAHypothesis
Keywordsstructural genomics / unknown function / NYSGXRC / SGX clone name 3174c1TCt3b1 / target T1521 / Hypothetical protein Ylba from E.Coli / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


(S)-ureidoglycine aminohydrolase / ureidoglycine aminohydrolase activity / purine nucleobase metabolic process / manganese ion binding / cytoplasm
Similarity search - Function
(S)-ureidoglycine aminohydrolase / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
(S)-ureidoglycine aminohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Thirumuruhan, R. / Ramagopal, U.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Ylba, hypothetical protein from E.Coli
Authors: Fedorov, A.A. / Fedorov, E.V. / Thirumuruhan, R. / Ramagopal, U.A. / Almo, S.C.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ylbA
B: Hypothetical protein ylbA


Theoretical massNumber of molelcules
Total (without water)57,5092
Polymers57,5092
Non-polymers00
Water0
1
A: Hypothetical protein ylbA


Theoretical massNumber of molelcules
Total (without water)28,7541
Polymers28,7541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein ylbA


Theoretical massNumber of molelcules
Total (without water)28,7541
Polymers28,7541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hypothetical protein ylbA
B: Hypothetical protein ylbA

A: Hypothetical protein ylbA
B: Hypothetical protein ylbA

A: Hypothetical protein ylbA
B: Hypothetical protein ylbA

A: Hypothetical protein ylbA
B: Hypothetical protein ylbA


Theoretical massNumber of molelcules
Total (without water)230,0358
Polymers230,0358
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area22670 Å2
ΔGint-119 kcal/mol
Surface area70540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.026, 109.026, 136.612
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a monomer

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Components

#1: Protein Hypothetical protein ylbA / Hypothesis


Mass: 28754.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YLBA, GLXB6, B0515 / Production host: Escherichia coli (E. coli) / References: UniProt: P75713

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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: 3.426 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 277 K / pH: 7
Details: DL-Malic acid, pH 7.0, VAPOR DIFFUSION, temperature 277.0K, pH 7.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98, 0.97934, 0.97911, 0.97166
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 22, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.979341
30.979111
40.971661
ReflectionResolution: 2.6→20 Å / Num. obs: 22935 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.8 / % possible all: 87.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1100 4.9 %RANDOM
Rwork0.232 ---
obs0.232 22935 93.6 %-
all-22935 --
Solvent computationSolvent model: FLAT MODE / Bsol: 33.9517 Å2 / ksol: 0.339398 e/Å3
Displacement parametersBiso mean: 47.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 0 0 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.871.5
X-RAY DIFFRACTIONc_mcangle_it7.612
X-RAY DIFFRACTIONc_scbond_it6.042
X-RAY DIFFRACTIONc_scangle_it9.42.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 114 4.6 %
Rwork0.361 1178 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ION.PARAMION.TOP
X-RAY DIFFRACTION2PROTEIN_REP.PARAM

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