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- PDB-2hr2: Crystal structure of a tpr-like protein (ct2138) from chlorobium ... -

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Basic information

Entry
Database: PDB / ID: 2hr2
TitleCrystal structure of a tpr-like protein (ct2138) from chlorobium tepidum tls at 2.54 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / Alpha-alpha superhelix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyDomain of Unknown Function DUF3856 / Domain of Unknown Function (DUF3856) / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / DUF3856 domain-containing protein
Function and homology information
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_663012.1) from Chlorobium tepidum TLS at 2.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE RESIDUES 1 TO 158.
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ...BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. DURING PURIFICATION, SOME DATA SUGGESTED THAT THE PROTEIN MAY REVERSIBLY FORM HIGHER ORDER OLIGOMERS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,87622
Polymers106,5726
Non-polymers1,30416
Water1,58588
1
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8542
Polymers17,7621
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8542
Polymers17,7621
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1666
Polymers17,7621
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8542
Polymers17,7621
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9824
Polymers17,7621
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1666
Polymers17,7621
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15460 Å2
ΔGint-76 kcal/mol
Surface area38820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.090, 91.280, 176.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYS4AA2 - 53 - 6
21MSEMSELYSLYS4BB1 - 52 - 6
31MSEMSELYSLYS4CC1 - 52 - 6
41MSEMSELYSLYS4DD1 - 52 - 6
51MSEMSELYSLYS4EE1 - 52 - 6
61MSEMSELYSLYS4FF1 - 52 - 6
12GLUGLUILEILE2AA6 - 1527 - 153
22GLUGLUILEILE2BB6 - 1527 - 153
32GLUGLUILEILE2CC6 - 1527 - 153
42GLUGLUILEILE2DD6 - 1527 - 153
52GLUGLUILEILE2EE6 - 1527 - 153
62GLUGLUILEILE2FF6 - 1527 - 153
13ALAALAALAALA4AA153 - 157154 - 158
23ALAALAALAALA4BB153 - 157154 - 158
33ALAALAALAALA4CC153 - 157154 - 158
43ALAALAALAALA4DD153 - 157154 - 158
53ALAALAALAALA4EE153 - 157154 - 158
63ALAALAGLYGLY4FF153 - 156154 - 157

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Hypothetical protein


Mass: 17762.000 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS / Gene: NP_663012.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KAL8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.54 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 25.0% Glycerol, 0.6M KH2PO4, 0.6M NaH2PO4, 0.1M HEPES, pH 7.5, 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: 0.91837, 0.97936, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.97921
ReflectionResolution: 2.54→29.696 Å / Num. obs: 47660 / % possible obs: 90.9 % / Redundancy: 2.18 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.54-2.632.150.5631.816175728780.6
2.63-2.740.4382.217679795983.5
2.74-2.860.3492.716989768786.8
2.86-3.010.2663.417870810489.6
3.01-3.20.1974.518774852091.8
3.2-3.440.1176.818472837993.8
3.44-3.790.0739.719508891995.8
3.79-4.330.0513.319170872696.2
4.330.0441519464884596.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHARPphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.54→29.696 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 20.249 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.24
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL SE-MET INCORPORATION. 3). GLYCEROL MOLECULES AND CHLORIDE ANIONS FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE STRUCTURE. 4). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2415 5.1 %RANDOM
Rwork0.204 ---
obs0.205 47611 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.893 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2--0.88 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.54→29.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 81 88 7224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227259
X-RAY DIFFRACTIONr_bond_other_d0.0020.026650
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9649763
X-RAY DIFFRACTIONr_angle_other_deg0.857315327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2925938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42323.769337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.041151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6061557
X-RAY DIFFRACTIONr_chiral_restr0.0740.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021500
X-RAY DIFFRACTIONr_nbd_refined0.2030.31637
X-RAY DIFFRACTIONr_nbd_other0.1370.36070
X-RAY DIFFRACTIONr_nbtor_refined0.1740.53537
X-RAY DIFFRACTIONr_nbtor_other0.0840.54026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.5203
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.326
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.54
X-RAY DIFFRACTIONr_mcbond_it0.88834879
X-RAY DIFFRACTIONr_mcbond_other0.28731942
X-RAY DIFFRACTIONr_mcangle_it0.98457280
X-RAY DIFFRACTIONr_scbond_it2.67382772
X-RAY DIFFRACTIONr_scangle_it3.8112481
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A49MEDIUM POSITIONAL0.750.5
12B49MEDIUM POSITIONAL0.30.5
13C49MEDIUM POSITIONAL0.230.5
14D49MEDIUM POSITIONAL0.270.5
15E49MEDIUM POSITIONAL0.330.5
16F49MEDIUM POSITIONAL0.30.5
11A49MEDIUM THERMAL0.422
12B49MEDIUM THERMAL0.162
13C49MEDIUM THERMAL0.192
14D49MEDIUM THERMAL0.232
15E49MEDIUM THERMAL0.182
16F49MEDIUM THERMAL0.312
21A862TIGHT POSITIONAL0.020.05
22B862TIGHT POSITIONAL0.020.05
23C862TIGHT POSITIONAL0.020.05
24D862TIGHT POSITIONAL0.020.05
25E862TIGHT POSITIONAL0.020.05
26F862TIGHT POSITIONAL0.020.05
21A1201MEDIUM POSITIONAL0.340.5
22B1201MEDIUM POSITIONAL0.40.5
23C1201MEDIUM POSITIONAL0.380.5
24D1201MEDIUM POSITIONAL0.450.5
25E1201MEDIUM POSITIONAL0.390.5
26F1201MEDIUM POSITIONAL0.290.5
21A862TIGHT THERMAL0.030.5
22B862TIGHT THERMAL0.030.5
23C862TIGHT THERMAL0.030.5
24D862TIGHT THERMAL0.040.5
25E862TIGHT THERMAL0.030.5
26F862TIGHT THERMAL0.030.5
21A1201MEDIUM THERMAL0.272
22B1201MEDIUM THERMAL0.262
23C1201MEDIUM THERMAL0.32
24D1201MEDIUM THERMAL0.322
25E1201MEDIUM THERMAL0.292
26F1201MEDIUM THERMAL0.262
31A51MEDIUM POSITIONAL0.220.5
32B51MEDIUM POSITIONAL0.280.5
33C51MEDIUM POSITIONAL0.240.5
34D51MEDIUM POSITIONAL0.530.5
35E51MEDIUM POSITIONAL0.490.5
36F51MEDIUM POSITIONAL0.360.5
31A51MEDIUM THERMAL0.132
32B51MEDIUM THERMAL0.272
33C51MEDIUM THERMAL0.182
34D51MEDIUM THERMAL0.362
35E51MEDIUM THERMAL0.372
36F51MEDIUM THERMAL0.352
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 195 -
Rwork0.329 3285 -
obs-3480 99.83 %
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)
14.58550.5922-2.05243.4791-1.31845.16860.3476-0.53490.74490.2904-0.1625-0.1227-0.72960.2442-0.1850.0235-0.10290.0035-0.0595-0.1566-0.072390.4450.91884.319
25.56441.67760.43693.0561-0.57522.6954-0.0391-0.04290.4703-0.03260.10020.2427-0.3895-0.1962-0.06110.08950.12210.1896-0.20030.168-0.103376.81557.11554.539
33.7149-0.91781.11172.7344-1.05626.10550.0741-0.38350.35110.19180.01930.1783-0.6202-0.364-0.0935-0.20830.03520.1216-0.17930.0225-0.124658.27643.09378.638
45.9233-0.07910.60011.9758-0.36852.53360.006-0.0871-0.4135-0.11940.00210.01620.1447-0.1383-0.0082-0.22130.0242-0.0259-0.17680.0962-0.178785.70621.08282.116
52.77270.4166-0.71752.7441-1.16065.45550.04580.2626-0.3779-0.3512-0.02220.07240.3811-0.1174-0.0236-0.18250.0242-0.0492-0.1647-0.0855-0.14765.05123.64356.044
65.20820.35381.86152.07140.43375.06420.12110.3773-0.2441-0.196-0.0294-0.32980.11140.4433-0.0916-0.11010.05720.1664-0.1675-0.0148-0.184496.59334.0553.433
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1573 - 158
22BB1 - 1572 - 158
33CC1 - 1572 - 158
44DD1 - 1572 - 158
55EE1 - 1572 - 158
66FF1 - 1562 - 157

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