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- PDB-1sc0: X-ray Structure of YB61_HAEIN Northeast Structural Genomics Conso... -

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Basic information

Entry
Database: PDB / ID: 1sc0
TitleX-ray Structure of YB61_HAEIN Northeast Structural Genomics Consortium Target IR63
ComponentsHypothetical protein HI1161
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative esterase HI_1161
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKuzin, A.P. / Lee, I. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray Structure of YB61_HAEIN Northeast Structural Genomics Consortium Target IR63.
Authors: Kuzin, A.P. / Lee, I. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
SupersessionNov 3, 2009ID: 1O0I
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein HI1161
B: Hypothetical protein HI1161


Theoretical massNumber of molelcules
Total (without water)30,4162
Polymers30,4162
Non-polymers00
Water4,378243
1
A: Hypothetical protein HI1161


Theoretical massNumber of molelcules
Total (without water)15,2081
Polymers15,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein HI1161


Theoretical massNumber of molelcules
Total (without water)15,2081
Polymers15,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.5, 60.9, 70.960
Angle α, β, γ (deg.)90.00, 134.5, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein HI1161


Mass: 15208.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI1161 / Plasmid: pIR63-21-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P45083
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM potassium sodium tartrate tetrahydrate, 18% PEG 3350, pH 7.5, 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 4 / Detector: CCD / Date: Feb 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 65061 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.78 Å / Rmerge(I) obs: 0.261 / % possible all: 95.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 191248.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2640 4.9 %RANDOM
Rwork0.203 ---
obs0.203 53748 82.2 %-
all-62531 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1938 Å2 / ksol: 0.357457 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å20 Å2-0.95 Å2
2---1.32 Å20 Å2
3----2.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 243 2335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 279 4.9 %
Rwork0.253 5452 -
obs--52.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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