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- PDB-2nwi: Crystal structure of protein AF1396 from Archaeoglobus fulgidus, ... -

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Basic information

Entry
Database: PDB / ID: 2nwi
TitleCrystal structure of protein AF1396 from Archaeoglobus fulgidus, Pfam DUF98
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyChorismate pyruvate-lyase Rv2949c-like / Chorismate pyruvate-lyase Rv2949c-like / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Adams, J. / Sridhar, V. / Wasserman, S. / Smith, D. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein O28875 from Archaeoglobus fulgidus
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Adams, J. / Sridhar, V. / Wasserman, S. / Smith, D. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
E: Hypothetical protein
F: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)121,1726
Polymers121,1726
Non-polymers00
Water8,809489
1
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)40,3912
Polymers40,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hypothetical protein
D: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)40,3912
Polymers40,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area15650 Å2
MethodPISA
3
E: Hypothetical protein
F: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)40,3912
Polymers40,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.131, 128.647, 129.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsprobable dimer

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Components

#1: Protein
Hypothetical protein /


Mass: 20195.305 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28875
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 46.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Bis-Tris, 30% PEG MME 550, 50mM calcium chloride, pH 6.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2006
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→19.881 Å / Num. all: 57882 / Num. obs: 57535 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.6 / Num. measured all: 55734 / Num. unique all: 8204 / Rsym value: 0.737 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.04 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.291 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2874 5 %RANDOM
Rwork0.208 ---
obs0.211 57472 99.43 %-
all-57801 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--1.41 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7809 0 0 489 8298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227924
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.96710661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4175955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83922.85407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85151568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.89315106
X-RAY DIFFRACTIONr_chiral_restr0.0930.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025866
X-RAY DIFFRACTIONr_nbd_refined0.2150.23334
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2520
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.219
X-RAY DIFFRACTIONr_mcbond_it0.7851.54970
X-RAY DIFFRACTIONr_mcangle_it1.25327701
X-RAY DIFFRACTIONr_scbond_it2.10833333
X-RAY DIFFRACTIONr_scangle_it3.5154.52955
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 224 -
Rwork0.238 3858 -
obs-4082 97.59 %

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