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- PDB-3htn: Crystal structure of a putative dna binding protein (bt_1116) fro... -

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Basic information

Entry
Database: PDB / ID: 3htn
TitleCrystal structure of a putative dna binding protein (bt_1116) from bacteroides thetaiotaomicron vpi-5482 at 1.50 A resolution
ComponentsPutative DNA binding protein
KeywordsMETAL BINDING PROTEIN / Duf269 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


PPC domain / Plants and Prokaryotes Conserved (PCC) domain / PPC domain profile profile. / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / PPC domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative DNA binding protein (NP_810029.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: Putative DNA binding protein
B: Putative DNA binding protein
C: Putative DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77519
Polymers50,6413
Non-polymers2,13316
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-200 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.688, 90.688, 53.888
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsTHE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Putative DNA binding protein


Mass: 16880.475 Da / Num. of mol.: 3 / Fragment: residues 38-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1116, NP_810029.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A8Q1

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Non-polymers , 5 types, 569 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 38-185 OF THE FULL LENGTH PROTEIN.

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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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 277 K / pH: 8
Details: 34.0000% polyethylene glycol 400, 0.2000M lithium sulfate, 0.1M TRIS pH 8.0, 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: 0.91837,0.97908,0.97840
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979081
30.97841
ReflectionResolution: 1.5→29.683 Å / Num. obs: 79258 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.77 % / Biso Wilson estimate: 16.81 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.56
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.6 / % possible all: 95.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.68 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.266 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061
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.SULPHATE ANIONS AND PEG MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE, RESPECTIVELY. 5.NI AND FE METAL IONS FROM PROTEIN EXPRESSION AND PURIFICATION ARE MODELED IN THE STRUCTURE. THE PRESENCE OF NI AND FE ARE SUPPORTED BY X-RAY FLUORESCENCE, BINDING GEOMETRY AND ANOMALOUS DIFFERENCE FOURIERS ABOVE AND BELOW THE NI AND FE ABSORPTION EDGE, RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3974 5 %RANDOM
Rwork0.143 ---
obs0.145 79234 99.8 %-
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 mean: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 96 553 3991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223811
X-RAY DIFFRACTIONr_bond_other_d0.0040.022544
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9675176
X-RAY DIFFRACTIONr_angle_other_deg1.13436236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89724.463177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.68815659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1321520
X-RAY DIFFRACTIONr_chiral_restr0.080.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024383
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02789
X-RAY DIFFRACTIONr_nbd_refined0.20.3643
X-RAY DIFFRACTIONr_nbd_other0.1770.32827
X-RAY DIFFRACTIONr_nbtor_refined0.1750.51869
X-RAY DIFFRACTIONr_nbtor_other0.0880.52230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5867
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.555
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70232491
X-RAY DIFFRACTIONr_mcbond_other0.4183951
X-RAY DIFFRACTIONr_mcangle_it2.35453766
X-RAY DIFFRACTIONr_scbond_it3.67871618
X-RAY DIFFRACTIONr_scangle_it5.05191410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 309 -
Rwork0.219 5515 -
obs--98.85 %
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)
10.6651-0.1160.39440.4066-0.39130.63630.0630.1431-0.0207-0.0942-0.1062-0.11670.14550.18210.04320.01420.04640.0115-0.00510.0062-0.022814.800529.9021.0218
20.9358-0.52080.06020.6127-0.20070.22980.0109-0.0879-0.07060.0992-0.0283-0.03470.06710.02570.01740.02550.0116-0.0189-0.03660.0149-0.017711.926822.207921.8894
30.3396-0.097-0.01650.5234-0.41140.42510.03130.0351-0.0545-0.0567-0.00240.10570.0601-0.0813-0.02890.0029-0.0204-0.0064-0.0314-0.0229-0.0072-5.782226.95829.4922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 185
2X-RAY DIFFRACTION2B43 - 185
3X-RAY DIFFRACTION3C43 - 185

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