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- PDB-1yoc: Crystal Structure of genomics APC5556 -

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Basic information

Entry
Database: PDB / ID: 1yoc
TitleCrystal Structure of genomics APC5556
Componentshypothetical protein PA1835
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PA1835 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Sulfur SAD
Function / homologyProtein of unknown function DUF4442 / Domain of unknown function (DUF4442) / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / DUF4442 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Sulfur SAD / Resolution: 1.7 Å
AuthorsDong, A. / Evdokimova, E. / Kudritskam, M. / Zhang, R.G. / Yakunin, A. / Pai, E. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of genomics AFPA1835 by Sulfur SAD methods
Authors: Dong, A. / Evdokimova, E. / Kudritskam, M. / Zhang, R.G. / Yakunin, A. / Pai, E. / Edwards, A. / Savchenko, A.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PA1835
B: hypothetical protein PA1835
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1433
Polymers32,0512
Non-polymers921
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-18 kcal/mol
Surface area12710 Å2
MethodPISA
2
A: hypothetical protein PA1835
B: hypothetical protein PA1835
hetero molecules

A: hypothetical protein PA1835
B: hypothetical protein PA1835
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2866
Polymers64,1014
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7140 Å2
ΔGint-48 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.162, 113.399, 58.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypothetical protein PA1835


Mass: 16025.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1835 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2R0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.31 Å3/Da / Density % sol: 46.33 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Na Formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97943 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 59643 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 7.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.47 / Num. unique all: 3096 / Rsym value: 0.685 / % possible all: 93.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: Sulfur SAD / Resolution: 1.7→40.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 364363.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1065 1.9 %RANDOM
Rwork0.167 ---
obs0.167 56253 89.6 %-
all-62747 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0547 Å2 / ksol: 0.373812 e/Å3
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2--1.2 Å20 Å2
3---0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 6 362 2602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 157 2.1 %
Rwork0.265 7189 -
obs-7189 70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3GLY.PARGLY.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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