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- PDB-1t1j: Crystal structure of genomics APC5043 -

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Basic information

Entry
Database: PDB / ID: 1t1j
TitleCrystal structure of genomics APC5043
Componentshypothetical protein
Keywordsstructural genomics / unknown function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHypothetical protein PA1492 / Domain of unknown function DUF1937 / Domain of unknown function (DUF1937) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DUF1937 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDong, A. / Xu, X. / Liu, Y. / Zhang, R. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Conserved Hypothetical Protein PA1492 from Pseudomonas aeruginosa
Authors: Dong, A. / Xu, X. / Liu, Y. / Zhang, R. / Savchenko, A. / Edwards, A.
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)28,7352
Polymers28,7352
Non-polymers00
Water2,630146
1
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)14,3671
Polymers14,3671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)14,3671
Polymers14,3671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: hypothetical protein

B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)28,7352
Polymers28,7352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
Buried area3000 Å2
ΔGint-33 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.500, 66.500, 116.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein hypothetical protein


Mass: 14367.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I3M0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.5M Sodium formate, 4% Ethylene, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.96411 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96411 Å / Relative weight: 1
ReflectionResolution: 1.7→31.98 Å / Num. all: 63515 / Num. obs: 59550 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 7.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.42 / Num. unique all: 6351 / Rsym value: 0.844 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→31.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 463098.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: maximum likelihood / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1090 1.8 %RANDOM
Rwork0.202 ---
all0.203 63515 --
obs0.202 59550 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6097 Å2 / ksol: 0.410827 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20.74 Å20 Å2
2---0.84 Å20 Å2
3---1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 0 146 2104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 138 1.6 %
Rwork0.284 8625 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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