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- PDB-1fux: CRYSTAL STRUCTURE OF E.COLI YBCL, A NEW MEMBER OF THE MAMMALIAN P... -

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Basic information

Entry
Database: PDB / ID: 1fux
TitleCRYSTAL STRUCTURE OF E.COLI YBCL, A NEW MEMBER OF THE MAMMALIAN PEBP FAMILY
ComponentsHYPOTHETICAL 19.5 KDA PROTEIN IN EMRE-RUS INTERGENIC REGION
KeywordsUNKNOWN FUNCTION / BETA PROTEIN
Function / homology
Function and homology information


outer membrane-bounded periplasmic space
Similarity search - Function
YbhB/YbcL / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
UPF0098 protein YbcL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSerre, L. / Pereira de Jesus, K. / Benedetti, H. / Bureaud, N. / Schoentgen, F. / Zelwer, C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of YBHB and YBCL from Escherichia coli, two bacterial homologues to a Raf kinase inhibitor protein.
Authors: Serre, L. / Pereira de Jesus, K. / Zelwer, C. / Bureaud, N. / Schoentgen, F. / Benedetti, H.
History
DepositionSep 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL 19.5 KDA PROTEIN IN EMRE-RUS INTERGENIC REGION
B: HYPOTHETICAL 19.5 KDA PROTEIN IN EMRE-RUS INTERGENIC REGION


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.425, 55.531, 60.152
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is a dimer constructed from chain A and chain B

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Components

#1: Protein HYPOTHETICAL 19.5 KDA PROTEIN IN EMRE-RUS INTERGENIC REGION


Mass: 17816.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PERIPLASMIC FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PIN-III-OMPA2 / Production host: Escherichia coli (E. coli) / Keywords: PERIPLASMIC FORM / References: UniProt: P77368
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMOLECULES 401, 402, 403, 404 HAVE BEEN MODELED BY HOH BUT CORRESPOND TO UNKNOWN MOLECULES PRESENT ...MOLECULES 401, 402, 403, 404 HAVE BEEN MODELED BY HOH BUT CORRESPOND TO UNKNOWN MOLECULES PRESENT IN THE BINDING SITES.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 6000, Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMHEPES1drop
21 mMdithiothreitol1drop
37.5 mg/mlprotein1drop
420-24 %(w/v)PEG60001reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97941
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.81→25 Å / Num. obs: 96044 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.894 Å2 / Rsym value: 0.03 / Net I/σ(I): 16.1
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 3751 / Rsym value: 0.088 / % possible all: 89.4
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 28148 / Num. measured all: 96044 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJJ E.COLI YBHB

1fjj


Resolution: 1.81→25 Å / SU B: 3.31573 / SU ML: 0.10434 / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / ESU R: 0.16318 / ESU R Free: 0.15721 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25423 2836 10 %RANDOM
Rwork0.1995 ---
obs-28872 97.5 %-
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.81→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 0 206 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.140.3
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor17.815
X-RAY DIFFRACTIONp_transverse_tor30.320
X-RAY DIFFRACTIONp_mcbond_it1.712
X-RAY DIFFRACTIONp_mcangle_it2.463
X-RAY DIFFRACTIONp_scbond_it2.182
X-RAY DIFFRACTIONp_scangle_it3.23
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_mcbond_it21.71
X-RAY DIFFRACTIONp_scbond_it22.18
X-RAY DIFFRACTIONp_mcangle_it32.46
X-RAY DIFFRACTIONp_scangle_it33.2

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