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- PDB-3urz: Crystal structure of a putative protein binding protein (BACOVA_0... -

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Basic information

Entry
Database: PDB / ID: 3urz
TitleCrystal structure of a putative protein binding protein (BACOVA_03105) from Bacteroides ovatus ATCC 8483 at 2.19 A resolution
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / TETRATRICOPEPTIDE REPEATS (TPR) CONTAINING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


: / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Tetratricopeptide repeat protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_03105) from Bacteroides ovatus ATCC 8483 at 2.19 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Feb 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 / 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.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.value / _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_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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5088
Polymers48,9902
Non-polymers5186
Water99155
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6263
Polymers24,4951
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8825
Polymers24,4951
Non-polymers3874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.703, 41.597, 236.878
Angle α, β, γ (deg.)90.000, 92.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A22 - 226
2115B22 - 226
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein


Mass: 24495.137 Da / Num. of mol.: 2 / Fragment: UNP residues 21-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_03105 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LZ30
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-227 OF 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.93
Details: 0.20 M zinc acetate, 16.40 % polyethylene glycol 8000, 0.1M MES pH 5.93, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.98021,0.97963
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 22, 2010
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.980211
30.979631
ReflectionResolution: 2.19→29.581 Å / Num. obs: 29857 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.56 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 10.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.21-2.290.4512.1107675529194.2
2.29-2.380.3962.5109735661196.2
2.38-2.490.2833.4110135683195.4
2.49-2.620.2154.4110685639195.9
2.62-2.780.1575.8110395587195.4
2.78-30.1028.3111235717195.1
3-3.30.06412104355415192.7
3.3-3.770.03518.9104655304189.4
3.77-4.740.02526102215232188.7
4.74-29.5810.02228.2105605413189.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMay 10, 2010data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.19→29.581 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.778 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. PRESENCE OF ZINC IN CRYSTALLIZATION CONDITION AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZINC (ZN) IONS. 7. PEG FRAGMENT (PG4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 1508 5.1 %RANDOM
Rwork0.2173 ---
obs0.2184 29857 95.57 %-
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 max: 244.13 Å2 / Biso mean: 101.8585 Å2 / Biso min: 41.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å21.32 Å2
2---1.12 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.19→29.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 18 55 3351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023371
X-RAY DIFFRACTIONr_bond_other_d0.0020.022335
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9754537
X-RAY DIFFRACTIONr_angle_other_deg1.19735703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5145414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.78924.817164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.20515643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4431522
X-RAY DIFFRACTIONr_chiral_restr0.090.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02670
X-RAY DIFFRACTIONr_bond_it4.1447.5593371
X-RAY DIFFRACTIONr_bond_other0.9637.922335
X-RAY DIFFRACTIONr_angle_it5.85113.9054532
X-RAY DIFFRACTIONr_angle_others3.74914.7955703
X-RAY DIFFRACTIONr_torsion_it9.76930.9271243
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1193MEDIUM POSITIONAL0.280.5
1447LOOSE POSITIONAL0.515
1193MEDIUM THERMAL4.542
1447LOOSE THERMAL6.7410
LS refinement shellResolution: 2.191→2.248 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 81 -
Rwork0.253 1572 -
all-1653 -
obs--76.35 %
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)
12.1220.31811.03031.95-1.52697.2075-0.0281-0.68760.02320.245-0.0894-0.18480.4240.33780.11751.23670.0776-0.13960.9996-0.06870.2796-14.70412.397137.246
22.2149-0.7328-0.92722.17681.06434.51990.0960.64260.0129-0.3567-0.12660.03450.2697-0.16360.03070.3396-0.0197-0.05830.4930.02740.0899-11.16214.659216.239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 226
2X-RAY DIFFRACTION2B21 - 226

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