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- PDB-5cd6: Crystal structure of a TPR-domain containing protein (BDI_1685) f... -

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Basic information

Entry
Database: PDB / ID: 5cd6
TitleCrystal structure of a TPR-domain containing protein (BDI_1685) from Parabacteroides distasonis ATCC 8503 at 2.26 A resolution
ComponentsTPR-domain containing protein
KeywordsUNKNOWN FUNCTION / TPR domain / Supersandwich domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF5107 / : / Domain of unknown function (DUF5107) / BDI_1685-like, C-terminal domain / metal ion binding / TPR-domain containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TPR-domain containing protein (BDI_1685) from Parabacteroides distasonis ATCC 8503 at 2.26 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Source and taxonomy
Category: citation_author / entity_src_gen / pdbx_struct_oper_list
Item: _citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR-domain containing protein
B: TPR-domain containing protein
C: TPR-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,50010
Polymers201,0643
Non-polymers4377
Water29,3641630
1
A: TPR-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1934
Polymers67,0211
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPR-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1533
Polymers67,0211
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TPR-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1533
Polymers67,0211
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: TPR-domain containing protein
B: TPR-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3477
Polymers134,0422
Non-polymers3045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-38 kcal/mol
Surface area44040 Å2
MethodPISA
5
C: TPR-domain containing protein
hetero molecules

C: TPR-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3076
Polymers134,0422
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4430 Å2
ΔGint-31 kcal/mol
Surface area43550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.480, 167.480, 312.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TPR-domain containing protein


Mass: 67021.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / NCTC 11152) (bacteria)
Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1685 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LCM3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1630 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (22-600) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-600) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2000M calcium acetate, 20.0000% polyethylene glycol 1000, 0.1M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97937,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979371
30.979221
ReflectionResolution: 2.26→29.715 Å / Num. obs: 125291 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 1.944 % / Biso Wilson estimate: 40.583 Å2 / Rmerge F obs: 0.992 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.106 / Net I/σ(I): 7.11 / Num. measured all: 460901
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.26-2.340.6340.44124701024488241630.608198.7
2.34-2.430.7320.3512.54543723730233730.48498.5
2.43-2.540.8110.27534739124729243800.37998.6
2.54-2.680.8860.2063.94926825861253140.28397.9
2.68-2.850.9280.1565.14698824886241950.21597.2
2.85-3.070.960.1156.64580524594235640.15995.8
3.07-3.370.980.089.24359624013225130.1193.8
3.37-3.860.9850.06111.94444124896229580.08492.2
3.86-4.850.9890.0513.74392424557226440.0792.2
4.85-29.7150.9940.03814.24704125040240010.05395.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 2.26→29.715 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9232 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 6420 5.15 %RANDOM
Rwork0.1746 ---
obs0.1763 124624 98.46 %-
Displacement parametersBiso max: 139.3 Å2 / Biso mean: 39.6338 Å2 / Biso min: 15.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.6472 Å20 Å20 Å2
2---0.5313 Å20 Å2
3---3.1785 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: LAST / Resolution: 2.26→29.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13974 0 22 1630 15626
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6505SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes363HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2044HARMONIC5
X-RAY DIFFRACTIONt_it14403HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1831SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17148SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14403HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg19628HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion2.77
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2468 467 5.04 %
Rwork0.2006 8793 -
all0.2029 9260 -
obs--98.46 %
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)
10.7175-0.3106-0.28350.5194-0.00480.76320.04120.0802-0.022-0.0559-0.0470.04590.011-0.15310.0058-0.08950.0429-0.0141-0.02390.0128-0.09136.668144.2464201.537
20.7221-0.24610.00510.70850.09010.7374-0.0079-0.0273-0.0169-0.00320.025-0.09440.12890.1412-0.0171-0.10330.0544-0.0003-0.05160.0067-0.087639.023928.2273215.785
30.480.0628-0.12830.91740.09541.0588-0.0267-0.01540.0739-0.04110.07870.0518-0.2437-0.1001-0.052-0.05710.0053-0.0052-0.0910.0272-0.122843.833317.8797148.688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|22 - 600}A22 - 600
2X-RAY DIFFRACTION2{B|22 - 600}B22 - 600
3X-RAY DIFFRACTION3{C|22 - 600}C22 - 600

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