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- PDB-1xm5: Crystal structure of metal-dependent hydrolase ybeY from E. coli,... -

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Basic information

Entry
Database: PDB / ID: 1xm5
TitleCrystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054
ComponentsHypothetical UPF0054 protein ybeY
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / NYSGXRC target T842 / PFAM family UPF0054 / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


: / nickel cation binding / maturation of SSU-rRNA / transcription antitermination / ribosomal small subunit biogenesis / metalloendopeptidase activity / rRNA processing / RNA endonuclease activity, producing 3'-phosphomonoesters / ribosome biogenesis / response to heat ...: / nickel cation binding / maturation of SSU-rRNA / transcription antitermination / ribosomal small subunit biogenesis / metalloendopeptidase activity / rRNA processing / RNA endonuclease activity, producing 3'-phosphomonoesters / ribosome biogenesis / response to heat / Hydrolases; Acting on ester bonds / translation / zinc ion binding / cytoplasm
Similarity search - Function
Metalloproteases ("zincins"), catalytic domain / Endoribonuclease YbeY, conserved site / Uncharacterized protein family UPF0054 signature. / Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Endoribonuclease YbeY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Shi, W. / Ramagopal, U.A. / Thirumuruhan, R. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The ybeY protein from Escherichia coli is a metalloprotein.
Authors: Zhan, C. / Fedorov, E.V. / Shi, W. / Ramagopal, U.A. / Thirumuruhan, R. / Manjasetty, B.A. / Almo, S.C. / Fiser, A. / Chance, M.R. / Fedorov, A.A.
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 UPF0054 protein ybeY
B: Hypothetical UPF0054 protein ybeY
C: Hypothetical UPF0054 protein ybeY
D: Hypothetical UPF0054 protein ybeY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3938
Polymers70,1584
Non-polymers2354
Water0
1
A: Hypothetical UPF0054 protein ybeY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5982
Polymers17,5401
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical UPF0054 protein ybeY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5982
Polymers17,5401
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical UPF0054 protein ybeY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5982
Polymers17,5401
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical UPF0054 protein ybeY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5982
Polymers17,5401
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.073, 119.613, 132.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein
Hypothetical UPF0054 protein ybeY


Mass: 17539.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybeY / Production host: Escherichia coli (E. coli) / References: UniProt: P0A898
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 51.1 %
Description: Radiation sources NSLS X9A and APS 19BM were used at early stages of the study.
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, magnesium chloride, Bis Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.97919
SYNCHROTRONNSLS X29A20.97938, 0.97919, 0.96408
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 28, 2004
MARRESEARCH2CCDJun 28, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979191
20.979381
30.964081
ReflectionResolution: 2.7→25 Å / Num. all: 20911 / Num. obs: 20911 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.7→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 894 Random
Rwork0.234 --
all0.239 18232 -
obs0.239 18232 -
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 4 0 4781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2

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