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- PDB-3hrg: Crystal structure of Bacteroides thetaiotaomicron BT_3980, protei... -

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Entry
Database: PDB / ID: 3hrg
TitleCrystal structure of Bacteroides thetaiotaomicron BT_3980, protein with actin-like ATPase fold and unknown function (NP_812891.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.85 A resolution
Componentsuncharacterized protein BT_3980 with actin-like ATPase fold
Keywordsstructural genomics / unknown function / NP_812891.1 / Bacteroides thetaiotaomicron BT_3980 / protein with actin-like ATPase fold and unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Protein of unknown function DUF3822, N-terminal domain / Protein of unknown function DUF3822, C-terminal domain / Protein of unknown function DUF3822 / Protein of unknown function (DUF3822) / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Unknown ligand / DUF3822 family protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Bacteroides thetaiotaomicron BT_3980, protein with actin-like ATPase fold and unknown function (NP_812891.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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 / 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein BT_3980 with actin-like ATPase fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9944
Polymers30,8261
Non-polymers1683
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.706, 91.181, 48.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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 BT_3980 with actin-like ATPase fold


Mass: 30825.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3980, NP_812891.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A0P1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (1-256) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THIS CONSTRUCT (1-256) WAS EXPRESSED WITH THE 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2000M K3Citrate, 20.0000% PEG-3350, No Buffer pH 8.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / 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
10.911621
20.979321
30.979181
ReflectionResolution: 1.85→29.579 Å / Num. obs: 25125 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.58 % / Biso Wilson estimate: 25.003 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.85-1.920.4451.890674785196
1.92-1.990.3162.581374272198.8
1.99-2.080.2093.889944693198.6
2.08-2.190.1535.190584725199.2
2.19-2.330.1186.892204803198.6
2.33-2.510.0829.290474701199
2.51-2.760.05612.889794647199
2.76-3.160.0342091684731199
3.16-3.980.01834.591144706198.6
3.98-29.5790.0144690714672197.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.579 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 6.989 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. ELECTRON DENSITY RESEMBLING CITRATE WAS OBSERVED AT THE PUTATIVE ACTIVE SITE. HOWEVER, BECAUSE REFINEMENT ATTEMPTS WITH THIS DENSITY MODELED AS A CITRATE DID NOT ACCOUNT FOR ALL OF THE OBSERVED DENSITY, AN UNIDENTIFIED LIGAND (UNL) WAS MODELED AT THIS LOCATION INSTEAD. 5. ETHYLENE GLYCOL (EDO) AND A POLYETHYLENE GLYCOL (PEG) FRAGMENT FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 6. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1277 5.1 %RANDOM
Rwork0.193 ---
obs0.195 25091 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.26 Å2 / Biso mean: 16.586 Å2 / Biso min: 2.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 19 246 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222436
X-RAY DIFFRACTIONr_bond_other_d0.0020.021670
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9633333
X-RAY DIFFRACTIONr_angle_other_deg1.13934121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.385327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64324.961127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39615471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7911513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022781
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02511
X-RAY DIFFRACTIONr_mcbond_it0.61.51436
X-RAY DIFFRACTIONr_mcbond_other0.1471.5568
X-RAY DIFFRACTIONr_mcangle_it1.09922364
X-RAY DIFFRACTIONr_scbond_it1.78131000
X-RAY DIFFRACTIONr_scangle_it2.8844.5942
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 96 -
Rwork0.286 1692 -
all-1788 -
obs--98.24 %
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)
14.0229-3.3427-1.95435.14361.50442.40140.03710.2311-0.1945-0.0152-0.15540.2845-0.0311-0.27160.11820.10570.01370.00240.07830.00730.092448.25832.91813.138
27.6167-0.9665-3.74842.39142.04143.79180.08290.12550.222-0.13140.0404-0.3197-0.2751-0.0243-0.12340.14120.00850.02420.06310.02520.197460.89135.15210.122
31.5139-0.33310.07684.70060.21441.5394-0.0757-0.11730.14190.39630.0053-0.31080.01110.07480.07040.07460.0161-0.03950.0483-0.0030.046964.08215.46617.979
46.06924.31262.92866.0223.74212.93870.0244-0.15190.13210.2266-0.29430.4315-0.0413-0.47850.26990.13270.03740.02010.1837-0.02820.16550.01514.60612.227
52.36850.6270.25153.69811.00323.9102-0.0970.05440.0545-0.1654-0.11860.1650.0236-0.20220.21570.03190.00470.00120.0207-0.01410.063753.3276.265-2.4
65.01896.77976.898211.311811.420311.5348-0.3065-0.30210.74530.2031-0.15070.43610.1614-0.14460.45720.51930.0379-0.01040.2798-0.06320.412547.20120.7176.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 67
3X-RAY DIFFRACTION3A68 - 137
4X-RAY DIFFRACTION4A138 - 155
5X-RAY DIFFRACTION5A156 - 240
6X-RAY DIFFRACTION6A241 - 256

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