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- PDB-3bdr: Crystal structure of fatty acid-binding protein-like Ycf58 from T... -

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Basic information

Entry
Database: PDB / ID: 3bdr
TitleCrystal structure of fatty acid-binding protein-like Ycf58 from Thermosynecoccus elongatus. Northeast Structural Genomics Consortium target TeR13.
ComponentsYcf58 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Ycf58 / Q8DI91 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Lyases / lyase activity
Similarity search - Function
Chromophore lyase CpcS/CpeS / CpeS-like protein / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chromophore lyase CpcS/CpeS
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: The crystal structure of fatty acid-binding protein-like Ycf58 from Thermosynecoccus elongatus.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 30, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Ycf58 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9722
Polymers21,8771
Non-polymers951
Water181
1
A: Ycf58 protein
hetero molecules

A: Ycf58 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9454
Polymers43,7552
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.014, 75.014, 83.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ycf58 protein


Mass: 21877.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: BP-1 / Gene: ycf58, tll1699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DI91
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 18% PEG 20000, 0.1M NH4H2PO4, 0.1M CAPS, 20% Glycerol, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 11252 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 28.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1113 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.4 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 105173.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. BULK SOLVENT MODEL USED in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.262 522 5.1 %RANDOM
Rwork0.236 ---
obs0.236 10246 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7207 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 66.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2---2.62 Å20 Å2
3---5.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 5 1 1231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 79 5.3 %
Rwork0.312 1410 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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