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- PDB-1fjj: CRYSTAL STRUCTURE OF E.COLI YBHB PROTEIN, A NEW MEMBER OF THE MAM... -

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Basic information

Entry
Database: PDB / ID: 1fjj
TitleCRYSTAL STRUCTURE OF E.COLI YBHB PROTEIN, A NEW MEMBER OF THE MAMMALIAN PEBP FAMILY
ComponentsHYPOTHETICAL 17.1 KDA PROTEIN IN MODC-BIOA INTERGENIC REGION
KeywordsLIPID BINDING PROTEIN / PEPB family
Function / homology
Function and homology information


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 YbhB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 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
DepositionAug 8, 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 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL 17.1 KDA PROTEIN IN MODC-BIOA INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6482
Polymers17,4101
Non-polymers2381
Water3,675204
1
A: HYPOTHETICAL 17.1 KDA PROTEIN IN MODC-BIOA INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 17.1 KDA PROTEIN IN MODC-BIOA INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2964
Polymers34,8192
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)85.470, 85.470, 73.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

Detailsthe biological assembly is a dimer constructed from chain A and a symmetry partner generated by a crystallography two-fold (the dimer has been suggested by gel filtration results)

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Components

#1: Protein HYPOTHETICAL 17.1 KDA PROTEIN IN MODC-BIOA INTERGENIC REGION


Mass: 17409.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Plasmid: PET14 / References: UniProt: P12994
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.3 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMHEPES1drop
32 mMdithiothreitol1drop
41.25-1.40 Mtrisodium citrate dihydrate1reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97947
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.66→25 Å / Num. all: 165834 / Num. obs: 165834 / % possible obs: 96.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.045 / Net I/σ(I): 13.6
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4024 / Rsym value: 0.44 / % possible all: 76.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 35266 / Num. measured all: 165834 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.66→25 Å / SU B: 1.3209 / SU ML: 0.04432 / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / ESU R: 0.07339 / ESU R Free: 0.07309 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19681 3522 10 %RANDOM
Rwork0.17978 ---
all-36545 --
obs-31740 96.2 %-
Displacement parametersBiso mean: 22.7 Å2
Refinement stepCycle: LAST / Resolution: 1.66→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 15 204 1433
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_plane_restr0.02130.03
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2310.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.0880.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor10.17
X-RAY DIFFRACTIONp_staggered_tor11.415
X-RAY DIFFRACTIONp_transverse_tor28.220
X-RAY DIFFRACTIONp_mcbond_it1.0232
X-RAY DIFFRACTIONp_mcangle_it1.5553
X-RAY DIFFRACTIONp_scbond_it1.8332
X-RAY DIFFRACTIONp_scangle_it2.7293
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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