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- PDB-1zx8: CRYSTAL STRUCTURE OF an atypical cyclophilin (peptidylprolyl cis-... -

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Basic information

Entry
Database: PDB / ID: 1zx8
TitleCRYSTAL STRUCTURE OF an atypical cyclophilin (peptidylprolyl cis-trans isomerase) (TM1367) FROM THERMOTOGA MARITIMA AT 1.90 A RESOLUTION
Componentshypothetical protein TM1367
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


TM1367-like / Cyclophilin TM1367-like domain / Cyclophilin-like / Cyclophilin - #20 / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Cyclophilin TM1367-like domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.
Authors: Jin, K.K. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, ...Authors: Jin, K.K. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Feuerhelm, J. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Hornsby, M. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C. / Stevens, R.C. / Spraggon, G. / van den Bedem, H. / Velasquez, J. / White, A. / Wolf, G. / Han, G.W. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM1367
B: hypothetical protein TM1367
C: hypothetical protein TM1367
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5387
Polymers46,7653
Non-polymers7744
Water4,378243
1
A: hypothetical protein TM1367
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8272
Polymers15,5881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein TM1367
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0653
Polymers15,5881
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: hypothetical protein TM1367
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6472
Polymers15,5881
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: hypothetical protein TM1367
hetero molecules

C: hypothetical protein TM1367
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2944
Polymers31,1772
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area3110 Å2
ΔGint-40 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.083, 132.875, 41.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: SER / Refine code: 6

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA-2 - 12410 - 136
2BB-2 - 12410 - 136
3CC-2 - 12310 - 135

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Components

#1: Protein hypothetical protein TM1367


Mass: 15588.306 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X187
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 46.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: 0.2M NaCl, 50.0% PEG-200, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.89194, 0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.891941
20.979341
ReflectionResolution: 1.9→29.08 Å / Num. obs: 34243 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.9-1.9599.83.70.61.224770.6
1.95-299.83.70.4331.724120.433
2-2.0699.83.70.359223820.359
2.06-2.121003.70.3062.422830.306
2.12-2.191003.70.245322510.245
2.19-2.271003.70.1953.821660.195
2.27-2.361003.70.1624.320960.162
2.36-2.451003.70.1295.120260.129
2.45-2.561003.70.1126.319530.112
2.56-2.691003.60.097718290.097
2.69-2.831003.60.0847.817750.084
2.83-31003.70.0728.716900.072
3-3.211003.60.0639.815870.063
3.21-3.471003.60.05410.914890.054
3.47-3.899.93.60.04812.313800.048
3.8-4.2599.83.60.04114.412320.041
4.25-4.9199.33.60.04213.511040.042
4.91-6.0199.23.50.041149480.041
6.01-8.598.43.30.0415.47440.04
8.5-29.0893.72.90.03810.24190.038

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.215 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. UNMODELED DENSITY NEAR A59 AND A81.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1729 5.1 %RANDOM
Rwork0.166 ---
all0.168 ---
obs-32474 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---2.4 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 49 243 3261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223088
X-RAY DIFFRACTIONr_bond_other_d0.0010.022850
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9754168
X-RAY DIFFRACTIONr_angle_other_deg1.44236649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48825.344131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8415525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.798159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined0.1980.2446
X-RAY DIFFRACTIONr_nbd_other0.1770.22823
X-RAY DIFFRACTIONr_nbtor_refined0.180.21435
X-RAY DIFFRACTIONr_nbtor_other0.090.21889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2195
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.215
X-RAY DIFFRACTIONr_mcbond_it2.4331973
X-RAY DIFFRACTIONr_mcbond_other0.6773776
X-RAY DIFFRACTIONr_mcangle_it3.23553090
X-RAY DIFFRACTIONr_scbond_it5.58181288
X-RAY DIFFRACTIONr_scangle_it7.389111078
Refine LS restraints NCS

Ens-ID: 1 / Number: 1850 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.445
2Bloose positional0.45
3Cloose positional0.485
1Aloose thermal2.6410
2Bloose thermal2.3410
3Cloose thermal3.0110
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 123 -
Rwork0.217 2352 -
obs--99.56 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16720.43330.18382.454-1.01921.61810.0148-0.0171-0.0153-0.0263-0.0725-0.1722-0.03030.10040.0577-0.0886-0.0008-0.0074-0.0864-0.0159-0.085449.352973.95439.5453
21.1168-0.59830.25733.3275-0.73521.92630.00260.10770.057-0.347-0.1069-0.08210.02150.03650.10430.0111-0.025-0.0004-0.0598-0.0017-0.07249.056498.2859.696
31.7263-0.07730.89392.66760.53011.73410.0808-0.12820.0143-0.1754-0.05710.0034-0.0414-0.1433-0.0237-0.06080.00130.0054-0.0379-0.00640.010845.0666123.044369.9762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 12410 - 136
2X-RAY DIFFRACTION2BB-2 - 12410 - 136
3X-RAY DIFFRACTION3CC-4 - 1238 - 135

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