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- PDB-3cnu: Crystal structure of the predicted coding region AF_1534 from Arc... -

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Basic information

Entry
Database: PDB / ID: 3cnu
TitleCrystal structure of the predicted coding region AF_1534 from Archaeoglobus fulgidus
ComponentsPredicted coding region AF_1534
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / coding region AF_1534 / Archaeoglobus fulgidus / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologySCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta / SCP2 domain-containing protein
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the predicted coding region AF_1534 from Archaeoglobus fulgidus.
Authors: Zhang, R. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Predicted coding region AF_1534


Theoretical massNumber of molelcules
Total (without water)13,1691
Polymers13,1691
Non-polymers00
Water1,60389
1
A: Predicted coding region AF_1534

A: Predicted coding region AF_1534


Theoretical massNumber of molelcules
Total (without water)26,3382
Polymers26,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3350 Å2
ΔGint-36.5 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.734, 57.614, 68.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Predicted coding region AF_1534


Mass: 13169.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304 / VC-16 / JCM 9628 / NBRC 100126 / Gene: GI:2649030, AF_1534 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O28738
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M Citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 26, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→44.15 Å / Num. all: 8588 / Num. obs: 8550 / % possible obs: 99.55 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.17
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2 / Num. unique all: 655 / % possible all: 96.49

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.512 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22195 433 4.8 %RANDOM
Rwork0.18304 ---
all0.18501 8550 --
obs0.18501 8550 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.4 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 0 89 960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022889
X-RAY DIFFRACTIONr_bond_other_d0.0010.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9621192
X-RAY DIFFRACTIONr_angle_other_deg0.83131520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4645109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33125.85441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.622152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
X-RAY DIFFRACTIONr_nbd_refined0.2140.2178
X-RAY DIFFRACTIONr_nbd_other0.1840.2605
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2414
X-RAY DIFFRACTIONr_nbtor_other0.0850.2435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.210
X-RAY DIFFRACTIONr_mcbond_it1.1931.5713
X-RAY DIFFRACTIONr_mcbond_other0.2021.5225
X-RAY DIFFRACTIONr_mcangle_it1.292870
X-RAY DIFFRACTIONr_scbond_it2.4873420
X-RAY DIFFRACTIONr_scangle_it3.6434.5322
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 19 -
Rwork0.23 613 -
obs-632 96.49 %
Refinement TLS params.Method: refined / Origin x: 7.934 Å / Origin y: 8.418 Å / Origin z: 13.14 Å
111213212223313233
T-0.0077 Å2-0.0119 Å2-0.0105 Å2--0.0479 Å2-0.0158 Å2---0.0386 Å2
L1.1067 °20.5768 °20.2939 °2-0.6058 °20.1331 °2--1.0271 °2
S0.0152 Å °-0.037 Å °-0.0226 Å °0.092 Å °-0.0256 Å °-0.0888 Å °-0.1222 Å °0.0572 Å °0.0104 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 301 - 30
2X-RAY DIFFRACTION1AA31 - 6031 - 60
3X-RAY DIFFRACTION1AA61 - 9061 - 90
4X-RAY DIFFRACTION1AA91 - 11091 - 110
5X-RAY DIFFRACTION1AB117 - 1961 - 80
6X-RAY DIFFRACTION1AB197 - 20581 - 89

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