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- PDB-4pcv: The structure of BdcA (YjgI) from E. coli -

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Basic information

Entry
Database: PDB / ID: 4pcv
TitleThe structure of BdcA (YjgI) from E. coli
ComponentsBdcA (YjgI)
KeywordsOXIDOREDUCTASE / NADP(H) oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / BdcA (YjgI) / :
Similarity search - Component
Biological speciesEscherichia coli P0299438.9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsPage, R. / Peti, W. / Lord, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB0952550 United States
CitationJournal: Plos One / Year: 2014
Title: BdcA, a protein important for Escherichia coli biofilm dispersal, is a short-chain dehydrogenase/reductase that binds specifically to NADPH.
Authors: Lord, D.M. / Baran, A.U. / Wood, T.K. / Peti, W. / Page, R.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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: BdcA (YjgI)
B: BdcA (YjgI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5967
Polymers49,7572
Non-polymers8395
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint4 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.058, 52.461, 69.807
Angle α, β, γ (deg.)90.00, 118.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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Components

#1: Protein BdcA (YjgI)


Mass: 24878.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli P0299438.9 (bacteria) / Gene: ECP02994389_4551 / Production host: Escherichia coli (E. coli) / References: UniProt: N3A304, UniProt: A0A0J9X1Z4*PLUS
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 50% (v/v) PEG-200, 0.1 M Tris pH 7.0, 0.05 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 26365 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 14.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
RefinementResolution: 2.05→47.8 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1332 5.05 %
Rwork0.2007 --
obs0.2017 26359 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 56 53 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022780
X-RAY DIFFRACTIONf_angle_d0.5913742
X-RAY DIFFRACTIONf_dihedral_angle_d10.808990
X-RAY DIFFRACTIONf_chiral_restr0.02438
X-RAY DIFFRACTIONf_plane_restr0.003483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12160.26591220.24062473X-RAY DIFFRACTION98
2.1216-2.20650.24121240.21412486X-RAY DIFFRACTION99
2.2065-2.30690.22721450.20322450X-RAY DIFFRACTION99
2.3069-2.42860.23211340.19042521X-RAY DIFFRACTION99
2.4286-2.58070.22831330.19182481X-RAY DIFFRACTION100
2.5807-2.77990.20521360.18672495X-RAY DIFFRACTION100
2.7799-3.05970.23651320.19792525X-RAY DIFFRACTION100
3.0597-3.50230.22171430.19692531X-RAY DIFFRACTION100
3.5023-4.4120.21051400.18352504X-RAY DIFFRACTION99
4.412-47.78860.2181230.21962561X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.40130.251-0.02041.4552-0.13731.95950.013-0.13560.06090.02690.02250.06630.1154-0.16150.00310.1865-0.04340.0080.17140.02620.148237.857919.037842.6549
22.75582.50170.90793.27140.79930.2996-0.13490.10620.0194-0.42620.1453-0.1092-0.15430.1131-0.0050.2539-0.02870.01880.2425-0.03210.237966.858133.149451.422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 231)
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 231)

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