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- PDB-3b09: Crystal structure of the N-domain of FKBP22 from Shewanella sp. SIB1 -

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Basic information

Entry
Database: PDB / ID: 3b09
TitleCrystal structure of the N-domain of FKBP22 from Shewanella sp. SIB1
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsCHAPERONE / Val-Leu zipper / helices
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain superfamily / Domain amino terminal to FKBP-type peptidyl-prolyl isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesShewanella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBudiman, C. / Angkawidjaja, C. / Motoike, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: dimer dissociation by disruption of Val-Leu knot
Authors: Budiman, C. / Angkawidjaja, C. / Motoike, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionJun 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)9,7071
Polymers9,7071
Non-polymers00
Water50428
1
A: Peptidyl-prolyl cis-trans isomerase

A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,4142
Polymers19,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4120 Å2
ΔGint-45 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.703, 39.703, 101.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / FKBP22 / FK506-binding protein


Mass: 9706.961 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella (bacteria) / Strain: SIB1 / Gene: fklB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q765B0, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M Na/K Phosphate, 20% PEG 1000, 0.2 M NaCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.97888, 0.97919, 0.96500
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979191
30.9651
ReflectionResolution: 1.9→50 Å / Num. obs: 7712 / % possible obs: 98.3 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Rsym value: 0.119 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6 / Num. unique all: 364 / Rsym value: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
BL44BSSdata collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→34.38 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.89 / SU B: 2.996 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27597 353 4.6 %RANDOM
Rwork0.23179 ---
obs0.23386 7299 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.51 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms487 0 0 28 515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022497
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.939669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.448566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.83325.225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.1071583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.891153
X-RAY DIFFRACTIONr_chiral_restr0.0820.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02385
X-RAY DIFFRACTIONr_mcbond_it2.1821.5322
X-RAY DIFFRACTIONr_mcangle_it3.8682507
X-RAY DIFFRACTIONr_scbond_it6.6823175
X-RAY DIFFRACTIONr_scangle_it10.0694.5161
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 26 -
Rwork0.278 521 -
obs--99.27 %

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