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- PDB-2pbc: FK506-binding protein 2 -

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Basic information

Entry
Database: PDB / ID: 2pbc
TitleFK506-binding protein 2
ComponentsFK506-binding protein 2
KeywordsISOMERASE / Endoplasmic reticulum / Polymorphism / Rotamase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP2/11 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase FKBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalker, J.R. / Neculai, D. / Davis, T. / Butler-Cole, C. / Sicheri, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Neculai, D. / Davis, T. / Butler-Cole, C. / Sicheri, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of FK506-Binding Protein 2
Authors: Walker, J.R. / Neculai, D. / Davis, T. / Butler-Cole, C. / Sicheri, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionMar 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FK506-binding protein 2
B: FK506-binding protein 2
C: FK506-binding protein 2
D: FK506-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1568
Polymers44,7314
Non-polymers4244
Water5,314295
1
A: FK506-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2892
Polymers11,1831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FK506-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2892
Polymers11,1831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FK506-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2892
Polymers11,1831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FK506-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2892
Polymers11,1831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.430, 39.335, 108.316
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FK506-binding protein 2 / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / 13 kDa FKBP / FKBP-13


Mass: 11182.800 Da / Num. of mol.: 4 / Fragment: Residues 43-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP2, FKBP13 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26885, peptidylprolyl isomerase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 32% PEG MME550, CRYOPROTECTED IN PARATONE-N, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→23.1 Å / Num. all: 32970 / Num. obs: 32970 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.044 / Net I/σ(I): 27.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 2860 / Rsym value: 0.155 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y0O
Resolution: 1.8→23.06 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.99 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.25986 1648 5 %RANDOM
Rwork0.18493 ---
obs0.18861 31311 98.32 %-
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: 21.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.12 Å2
2---0.92 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 0 329 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223220
X-RAY DIFFRACTIONr_angle_refined_deg1.6872.0084330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07724.062128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20115587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6651520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022416
X-RAY DIFFRACTIONr_nbd_refined0.2110.21412
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.239
X-RAY DIFFRACTIONr_mcbond_it1.47422091
X-RAY DIFFRACTIONr_mcangle_it2.08333230
X-RAY DIFFRACTIONr_scbond_it3.09841290
X-RAY DIFFRACTIONr_scangle_it4.0651100
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 89 -
Rwork0.194 1853 -
obs--79.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
112.09690.72132.10930.805-0.87771.6891-0.42370.35390.06230.18370.146-0.1432-0.24180.37080.2777-0.0016-0.02840.00830.1109-0.08320.107229.97565.594540.3355
23.51441.6196-1.558511.7301-5.409111.80480.07950.19820.07510.05970.1762-0.1046-0.1706-0.1028-0.25570.05050.0088-0.00760.074-0.02530.063121.4891-2.129438.7399
326.5719-11.4342-3.46995.01131.89867.7426-0.0507-0.98310.5256-0.3750.1336-0.2007-0.0161-0.5146-0.08290.1720.0203-0.032-0.02530.0088-0.02657.86611.200952.8798
416.9893-9.13114.14466.0781-1.422212.838-0.9064-0.7925-0.08660.87480.70090.4586-0.0781-1.16350.20550.21040.0650.08440.06640.08-0.00767.6256-2.047655.7669
50.64613.0819-0.061115.4457-4.355622.18230.50260.265-0.20012.01180.01510.1141-0.76110.2757-0.51770.320.07060.0208-0.01370.002-0.070516.8721-9.106550.4038
61.87510.21041.13817.56710.89220.7682-0.1005-0.01050.0345-0.19220.1930.5147-0.1008-0.0304-0.09250.02710.01010.00040.06970.04580.066713.82870.442738.8358
710.6626-8.3576-0.728912.52281.89230.665-0.4503-0.25450.09151.30870.4007-0.3314-0.05380.03330.04970.22760.041-0.02510.0119-0.0053-0.043121.04145.918348.2791
88.03050.9351-0.1731.2253-0.67070.38280.0314-0.0883-0.4448-0.19970.0803-0.02710.0877-0.2251-0.11170.04480.01970.03030.05220.02040.10131.27462.82442.5103
912.44684.7446-4.074553.9911-6.39577.7507-0.42120.0442-1.12941.2923-0.0792-1.12581.00030.19390.50040.0676-0.00070.03690.06790.16340.0781-2.3413-3.11548.4258
1017.3921-5.62680.13675.9409-0.72312.7905-0.318-0.10370.42510.16660.2149-0.3049-0.1799-0.18040.10320.10190.04150.0410.05750.03070.00537.45364.520149.8884
1128.052-10.7319-8.663113.07760.75494.5575-0.3457-0.5284-0.25641.50250.265-0.59940.07220.36730.08070.26260.0678-0.1078-0.0336-0.0169-0.009621.9325-0.919348.4418
123.1397-3.36894.292615.2267-13.868513.25730.06220.2105-0.3811-0.1834-0.5969-1.1954-0.03320.33450.5347-0.07480.034-0.03150.0112-0.02480.160129.3455-3.73939.8943
138.0316-1.2768-2.08131.50491.06050.9483-0.0165-0.23130.1653-0.0816-0.0650.1550.0413-0.26810.08150.01390.01140.01820.10870.01050.073111.216324.009114.7421
141.4937-0.4827-1.09582.7004-1.32113.5246-0.0502-0.22740.00910.07330.1164-0.02180.06790.2707-0.06610.0664-0.0044-0.01630.0771-0.01180.053420.078516.318311.7071
1525.530312.6642.43117.8374-1.09193.6258-0.31680.54660.269-0.09880.2868-0.0941-0.01270.16860.02990.01430.01930.00890.0928-0.07930.096833.242119.74252.2111
1612.70988.6329-2.011311.4792-5.54938.12020.00530.433-0.1964-0.13710.1151-0.5761-0.41010.2293-0.12040.0026-0.01040.01670.1083-0.09680.086638.338120.53870.6129
1710.592710.47784.048518.49264.33981.5612-0.05270.2117-0.047-0.19040.2695-0.50830.30140.0846-0.21670.06510.0039-0.00310.0849-0.02360.018526.904511.8731-1.4837
184.4449-2.1351-6.38321.31542.63979.79390.2684-0.00350.098-0.2999-0.1493-0.159-0.1564-0.3784-0.11910.0778-0.01190.01380.0897-0.00070.026623.650711.53648.3175
191.45850.58010.34213.0015-0.4690.22750.0662-0.0537-0.02660.2327-0.0931-0.11940.02580.00490.02690.05-0.0024-0.0070.0633-0.01120.037426.253820.177815.7916
207.02291.99052.53176.83350.08622.656-0.09160.02840.0048-0.0920.03790.3380.01390.10540.05360.06870.0057-0.01610.0749-0.00770.039919.77925.13255.1475
211.5551.06521.26841.2645-0.17583.0754-0.0346-0.0259-0.22540.08070.1131-0.1229-0.07070.0538-0.07840.018-0.0024-0.00040.0828-0.00120.076836.785623.738812.8539
2211.444816.179618.827224.098419.842668.41810.4219-0.3713-0.5359-0.04960.0006-0.96352.51221.5037-0.42240.00120.1283-0.05310.10130.00470.151544.115714.651111.6095
236.63971.24863.41971.896-0.48882.53260.03390.2842-0.273-0.14540.0694-0.26080.05590.3054-0.10330.04790.01640.0240.1047-0.05070.081637.023821.33296.1486
247.92832.5861-3.91193.6784-2.35796.3351-0.1003-0.1134-0.6377-0.18240.15790.38010.6341-0.3308-0.05760.0264-0.019-0.03170.04180.04520.131814.101216.17210.4752
2521.81320.5184-2.91990.38770.04220.424-0.061-0.18140.0066-0.039-0.12260.28890.0581-0.16640.18360.0069-0.0081-0.00790.09390.00270.06669.9573-6.259212.9505
262.1301-0.8218-3.82538.09414.607511.7580.03660.2368-0.0385-0.11470.1319-0.0146-0.0347-0.0271-0.16850.05010.00460.00320.0850.02020.059718.03871.343910.3662
2721.655-8.02055.31718.2797-2.6651.39670.1183-0.4507-0.4874-0.35090.22730.06950.01260.1142-0.34560.1077-0.00010.00760.0858-0.02660.009426.92740.579324.5888
2814.3466-9.2704-0.93148.4827-0.17484.4233-0.2357-0.66690.20250.25140.3539-0.27960.1530.3021-0.11820.064-0.0038-0.0320.0697-0.05240.001833.62440.259428.1758
292.5426-4.0036-0.49556.95125.455833.88360.21010.08310.28810.47590.12520.1067-0.274-0.1152-0.33520.1477-0.0370.02340.0224-0.00910.016422.63598.494523.2874
301.9441-0.08550.16422.3657-0.54040.17010.02340.0303-0.024-0.1011-0.0554-0.10390.04030.0630.0320.0570.01590.00410.0703-0.00630.038226.0972-1.143111.8363
316.4253-2.2382-1.76843.5402-1.65582.35630.08690.0522-0.09210.04320.00840.1958-0.1108-0.0499-0.09530.06880.00750.00120.0514-0.00230.009117.3537-5.943221.372
3217.23812.2562-5.7913.4091.40114.402-0.1742-0.2835-0.27460.06720.0489-0.04190.0059-0.03120.12530.05720.0246-0.03230.09250.00440.047933.0992-7.980618.903
3310.49070.87892.0216.05745.00185.15280.03780.15540.452-0.1820.0566-0.3154-0.3330.2698-0.09440.0860.0010.01640.08890.00880.089140.9359-0.892813.8475
343.0294-2.86844.43434.9714-0.688411.9539-0.1243-0.48470.49780.5159-0.1823-0.062-1.2063-0.05830.30660.0813-0.04480.01880.0766-0.12810.033442.16813.032521.7546
3511.7271-3.01740.67781.70910.12341.75350.0277-0.3456-0.09440.02470.05270.0936-0.0697-0.0372-0.08040.1141-0.0177-0.00350.06060.00420.060825.0303-2.510221.9747
365.2184.6949-2.108813.18239.406515.11630.4140.34550.70580.1023-0.39530.6269-0.3771-0.9613-0.0187-0.02050.06110.0230.05810.04410.076310.52653.017812.5218
376.1756-2.89021.05461.8569-1.00880.7065-0.03410.0388-0.78280.0551-0.2523-0.0778-0.10360.56740.2864-0.02190.0048-0.03520.1236-0.02680.121928.753214.711141.9151
384.8075-2.81370.88379.3789-1.8628.83330.0504-0.1873-0.12540.10510.38150.09460.0058-0.3638-0.43190.0564-0.0079-0.00170.0817-0.00790.085720.77822.305541.2766
398.06391.63910.02680.33330.02253.5261-0.18540.4187-0.00680.09440.13490.1512-0.1298-0.28460.05050.0423-0.0288-0.03660.07520.06420.07536.536920.295227.9671
402.6512.1756-0.43051.8962-1.826619.659-0.0374-0.29470.2921-0.3802-0.0571-0.1624-0.2403-0.07820.09460.1314-0.013-0.01410.04110.0450.043515.944228.353329.6979
411.34371.6337-0.7684.99441.20251.9558-0.125-0.03770.07960.34460.22710.54210.05620.0189-0.10210.00990.01910.03070.0470.04670.092712.397121.51642.9485
426.62710.3476-4.24174.69991.30885.62820.01230.0982-0.17660.16820.06440.140.1119-0.2319-0.07670.02710.0012-0.02410.06830.03430.066516.458314.088341.5423
4318.98659.5588.166912.41646.793412.5521-0.2245-0.0717-0.1796-0.82020.126-0.54730.4491-0.0510.09850.1417-0.01770.05750.0115-0.02150.00623.039414.489431.8875
447.0539-1.9746-1.92950.7825-0.19342.8698-0.0553-0.0034-0.0305-0.05810.08280.1191-0.0244-0.0854-0.02750.0274-0.0174-0.00550.00030.00550.1095.945713.854538.312
4512.74521.54670.871711.1208-4.565620.1729-0.2028-0.10420.22210.3180.26870.6488-1.2469-0.4867-0.06590.05680.01960.02610.0490.00380.0902-3.808424.10237.9761
463.55090.7493-2.68481.5763-1.42222.5461-0.11820.28360.21480.15470.09740.1589-0.0977-0.17490.02080.032-0.0023-0.03620.09540.02650.06910.392417.599234.6716
4735.66965.360610.80195.80361.56045.7672-0.10720.9062-0.3115-0.72070.2669-0.0663-0.0190.2063-0.15970.1378-0.02650.01820.0641-0.02220.033718.377117.8731.0101
482.65355.72910.81812.41122.39669.77230.2377-0.36590.45830.2424-0.2161-0.2263-0.39530.3808-0.0217-0.0373-0.02710.01410.0705-0.02370.158928.210823.841541.0018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA41 - 461 - 6
2X-RAY DIFFRACTION2AA47 - 547 - 14
3X-RAY DIFFRACTION3AA55 - 6115 - 21
4X-RAY DIFFRACTION4AA62 - 7122 - 31
5X-RAY DIFFRACTION5AA72 - 7732 - 37
6X-RAY DIFFRACTION6AA78 - 9638 - 56
7X-RAY DIFFRACTION7AA97 - 10357 - 63
8X-RAY DIFFRACTION8AA104 - 11664 - 76
9X-RAY DIFFRACTION9AA117 - 12577 - 85
10X-RAY DIFFRACTION10AA126 - 13086 - 90
11X-RAY DIFFRACTION11AA131 - 13591 - 95
12X-RAY DIFFRACTION12AA136 - 14096 - 100
13X-RAY DIFFRACTION13BB41 - 471 - 7
14X-RAY DIFFRACTION14BB48 - 558 - 15
15X-RAY DIFFRACTION15BB56 - 6016 - 20
16X-RAY DIFFRACTION16BB61 - 6721 - 27
17X-RAY DIFFRACTION17BB68 - 7328 - 33
18X-RAY DIFFRACTION18BB74 - 7834 - 38
19X-RAY DIFFRACTION19BB79 - 9639 - 56
20X-RAY DIFFRACTION20BB97 - 10357 - 63
21X-RAY DIFFRACTION21BB104 - 11364 - 73
22X-RAY DIFFRACTION22BB114 - 11974 - 79
23X-RAY DIFFRACTION23BB120 - 13180 - 91
24X-RAY DIFFRACTION24BB132 - 13992 - 99
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