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- PDB-4r7s: Crystal structure of a tetratricopeptide repeat protein (PARMER_0... -

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Basic information

Entry
Database: PDB / ID: 4r7s
TitleCrystal structure of a tetratricopeptide repeat protein (PARMER_03812) from Parabacteroides merdae ATCC 43184 at 2.39 A resolution
ComponentsTetratricopeptide repeat protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TPR family protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology: / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / NITRATE ION / DI(HYDROXYETHYL)ETHER / Tetratricopeptide repeat protein
Function and homology information
Biological speciesParabacteroides merdae ATCC 43184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.39 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a tetratricopeptide repeat protein (PARMER_03812) from Parabacteroides merdae ATCC 43184 at 2.39 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7229
Polymers30,1821
Non-polymers5418
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.676, 72.540, 109.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tetratricopeptide repeat protein /


Mass: 30181.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria)
Gene: PARMER_03812, ZP_02033777.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AK45
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (20-275) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (20-275) 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium nitrate 20.0% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: May 23, 2014
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: 2.39→39.676 Å / Num. obs: 13045 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.602 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.39-2.480.8420.6062.46496134613450.6899.9
2.48-2.570.9140.48235661114611450.53999.9
2.57-2.690.9330.3693.86400133513340.41599.9
2.69-2.830.960.2785.36227127812760.31299.8
2.83-3.010.9790.1917.36258130313030.215100
3.01-3.240.9930.11711.26113128012790.13199.9
3.24-3.570.9970.07716.36205132913170.08699.1
3.57-4.080.9970.05422.85662129312310.06295.2
4.08-5.120.9990.0427.96191133013280.04599.8
5.120.9990.03730.16298146614520.04299

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.39→39.676 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9031 / Occupancy max: 1 / Occupancy min: 0.15 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE EXPERIMENTAL (MAD) PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NITRATE (NO3) AND PEG FRAGMENTS (PEG) FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 660 5.08 %RANDOM
Rwork0.1896 ---
obs0.1922 13002 99.38 %-
Displacement parametersBiso max: 135.89 Å2 / Biso mean: 49.5632 Å2 / Biso min: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1--6.6036 Å20 Å20 Å2
2---1.4247 Å20 Å2
3---8.0283 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 2.39→39.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 35 156 2263
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1059SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes307HARMONIC5
X-RAY DIFFRACTIONt_it2167HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion274SEMIHARMONIC5
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_contact2687SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2167HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2908HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion3.13
LS refinement shellResolution: 2.39→2.58 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.26 137 5.21 %
Rwork0.2011 2495 -
all0.204 2632 -
obs--99.38 %
Refinement TLS params.Method: refined / Origin x: 11.0897 Å / Origin y: 49.6573 Å / Origin z: 79.123 Å
111213212223313233
T0.0498 Å20.0201 Å2-0.0232 Å2--0.0623 Å2-0.007 Å2---0.0837 Å2
L0 °2-0.0775 °2-0.126 °2-0.5215 °20.5208 °2--0.7831 °2
S-0.0192 Å °0.0645 Å °-0.0003 Å °-0.0927 Å °-0.099 Å °0.0435 Å °0.0202 Å °-0.0909 Å °0.1182 Å °
Refinement TLS groupSelection details: { A|0 - 274 }

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