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- PDB-2huh: Crystal structure of a duf2027 family protein (bt_2179) from bact... -

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Basic information

Entry
Database: PDB / ID: 2huh
TitleCrystal structure of a duf2027 family protein (bt_2179) from bacteroides thetaiotaomicron at 1.54 A resolution
ComponentsPutative DNA mismatch repair protein
KeywordsUNKNOWN FUNCTION / Putative dna mismatch repair protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Smr-associated-like / Domain of unknown function DUF2027 / Smr-associated-like superfamily / Domain of unknown function (DUF2027) / Smr domain / Smr domain superfamily / Smr domain / Smr domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA mismatch repair protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of putative DNA Mismatch Repair Protein (NP_811092.1) from Bacteroides Thetaiotaomicron VPI-5482 at 1.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_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_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_type.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: Putative DNA mismatch repair protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9642
Polymers16,9401
Non-polymers241
Water2,936163
1
A: Putative DNA mismatch repair protein
hetero molecules

A: Putative DNA mismatch repair protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9284
Polymers33,8802
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)43.043, 43.043, 167.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative DNA mismatch repair protein


Mass: 16939.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: NP_811092.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A5Q9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 12.0% PEG-3000, 0.2M NaCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97922,0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 2, 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
20.979221
30.979051
ReflectionResolution: 1.5→30.002 Å / Num. obs: 23849 / % possible obs: 97.6 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.54-1.584.20.7671667916010.76792.7
1.58-1.625.10.5851.3841416360.58595.5
1.62-1.676.30.4921.61010816050.49296.4
1.67-1.726.20.3991.9984115860.39996.5
1.72-1.786.30.2792.7952915070.27996.9
1.78-1.846.30.2193.5941014990.21997.1
1.84-1.916.20.1694.4892714340.16997.4
1.91-1.996.30.135.4864713720.1397
1.99-2.086.30.1115.7841813450.11197.4
2.08-2.187.70.1175.61000112960.11797.7
2.18-2.39.80.1215.41218812490.12199.6
2.3-2.4311.70.10861411012060.108100
2.43-2.613.20.16.31480911190.199.9
2.6-2.8113.40.0956.81417410600.095100
2.81-3.0813.30.0827.41344710080.082100
3.08-3.4413.50.0688.6120158900.068100
3.44-3.9813.20.0629.9106878080.062100
3.98-4.87130.05610.991457040.056100
4.87-6.8912.50.05111.671135710.051100
6.89-30.0110.50.04512.437193530.04598.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.54→30.002 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.722 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075
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 THE ...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 S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. MODEL REPRESENTS A PROTEOLYTIC FRAGMENT OF THE FULL-LENGTH PROTEIN, THOUGH THE EXACT BOUNDRIES ARE UNKOWN. RESIDUES 81-227 ARE MODELED BASED ON DENSITY. 5. UNKNOWN DENSITY NEAR ASP 89 WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1216 5.1 %RANDOM
Rwork0.166 ---
obs0.168 23764 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.54→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 1 163 1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221254
X-RAY DIFFRACTIONr_bond_other_d0.0010.021121
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9681727
X-RAY DIFFRACTIONr_angle_other_deg0.74232620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6455166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18825.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.205153
X-RAY DIFFRACTIONr_chiral_restr0.0940.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_nbd_refined0.1990.2200
X-RAY DIFFRACTIONr_nbd_other0.1740.21100
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2618
X-RAY DIFFRACTIONr_nbtor_other0.0830.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.217
X-RAY DIFFRACTIONr_mcbond_it1.9663816
X-RAY DIFFRACTIONr_mcbond_other0.4293303
X-RAY DIFFRACTIONr_mcangle_it2.54851255
X-RAY DIFFRACTIONr_scbond_it4.3668542
X-RAY DIFFRACTIONr_scangle_it6.09611462
LS refinement shellResolution: 1.539→1.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 75 -
Rwork0.261 1506 -
obs-1581 91.07 %
Refinement TLS params.Method: refined / Origin x: 2.257 Å / Origin y: 10.604 Å / Origin z: 53.878 Å
111213212223313233
T0.0812 Å20.0101 Å2-0.0133 Å2-0.0311 Å2-0.0022 Å2--0.0245 Å2
L0.6646 °20.3927 °20.5166 °2-0.8039 °20.4366 °2--1.2147 °2
S-0.0486 Å °-0.0482 Å °0.0458 Å °0.0318 Å °0.021 Å °-0.013 Å °-0.1017 Å °-0.0553 Å °0.0276 Å °
Refinement TLS groupSelection: ALL

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