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- PDB-2p17: Crystal structure of GK1651 from Geobacillus kaustophilus -

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Basic information

Entry
Database: PDB / ID: 2p17
TitleCrystal structure of GK1651 from Geobacillus kaustophilus
ComponentsPirin-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GK1651 / Geobacillus Kaustophilus / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / Protein Structure Initiative / SECSG / RIKEN Structural Genomics/Proteomics Initiative / RSGI / PSI
Function / homology
Function and homology information


Pirin, C-terminal domain / Pirin C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Pirin-like protein
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsZhu, J. / Swindell II, J.T. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Rose, J.P. / Wang, B.C. ...Zhu, J. / Swindell II, J.T. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of GK1651 from Geobacillus kaustophilus
Authors: Zhu, J. / Swindell II, J.T. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Rose, J.P. / Wang, B.C.
History
DepositionMar 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 13, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / refine / software
Item: _refine.pdbx_method_to_determine_struct / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pirin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5152
Polymers31,4591
Non-polymers561
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.571, 59.823, 69.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pirin-like protein


Mass: 31459.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1651 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q5KZF0
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.79 Å3/Da / Density % sol: 31.4 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: MICROBATCH USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (5.09 mg/ml) AND SOLUTION CONTAING 30% w/v PEG 4000, 0.1 M SODIUM ACETATE, 0.2 M AMMONIUM ACETATE PH 4.6, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 35234 / Num. obs: 35234 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rsym value: 0.061
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 22.5 / Num. unique all: 3479 / Rsym value: 0.17 / % possible all: 100

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Processing

Software
NameVersionClassification
SGXPROmodel building
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→19.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.19 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21313 1766 5 %RANDOM
Rwork0.18841 ---
obs0.18966 33392 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.52→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 1 211 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221977
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9522680
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20523.70889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70515327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0441515
X-RAY DIFFRACTIONr_chiral_restr0.0740.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.2811
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21330
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.51266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10321999
X-RAY DIFFRACTIONr_scbond_it1.9253796
X-RAY DIFFRACTIONr_scangle_it2.9094.5681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 133 -
Rwork0.203 2370 -
obs--99.17 %

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