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- PDB-1wuf: Crystal structure of protein GI:16801725, member of Enolase super... -

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Basic information

Entry
Database: PDB / ID: 1wuf
TitleCrystal structure of protein GI:16801725, member of Enolase superfamily from Listeria innocua Clip11262
Componentshypothetical protein lin2664
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NYSGXRC TARGET T2186 / enolase superfamily / New York SGX Research Center for Structural Genomics / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / menaquinone biosynthetic process / magnesium ion binding
Similarity search - Function
o-Succinylbenzoate synthase, MenC type 2 / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...o-Succinylbenzoate synthase, MenC type 2 / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
o-succinylbenzoate synthase
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Yew, W.S. / Gerlt, J.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family
Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. ...Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. / Swaminathan, S. / Burley, S.K. / Almo, S.C. / Glasner, M.E.
History
DepositionDec 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 11, 2014Group: Database references
Revision 1.4Jun 18, 2014Group: Other
Revision 1.5Dec 24, 2014Group: Database references
Revision 1.6Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.7Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.8Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein lin2664
B: hypothetical protein lin2664
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9894
Polymers88,9402
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-29 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.721, 87.346, 161.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein lin2664


Mass: 44470.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Production host: Escherichia coli (E. coli) / References: UniProt: Q927X3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.173 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG 3350, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. all: 17155 / Num. obs: 17155 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 91

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 811 RANDOM
Rwork0.236 --
all0.239 17155 -
obs0.239 17155 -
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5892 0 2 0 5894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.46

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