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- PDB-1j5y: Crystal structure of transcriptional regulator (TM1602) from Ther... -

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Basic information

Entry
Database: PDB / ID: 1j5y
TitleCrystal structure of transcriptional regulator (TM1602) from Thermotoga maritima at 2.3 A resolution
ComponentsTRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / TM1602 / TRANSCRIPTIONAL REGULATOR / BIOTIN REPRESSOR FAMILY / JCSG / CONSERVED HYPOTHETICAL PROTEIN / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
3H domain / 3H domain / Transcription repressor NadR / 3H domain superfamily / 3H domain / Helix-turn-helix, type 11 / HTH domain / Histidine-containing Protein; Chain: A; / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...3H domain / 3H domain / Transcription repressor NadR / 3H domain superfamily / 3H domain / Helix-turn-helix, type 11 / HTH domain / Histidine-containing Protein; Chain: A; / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / Probable transcription repressor NiaR
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution.
Authors: Weekes, D. / Miller, M.D. / Krishna, S.S. / McMullan, D. / McPhillips, T.M. / Acosta, C. / Canaves, J.M. / Elsliger, M.A. / Floyd, R. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / ...Authors: Weekes, D. / Miller, M.D. / Krishna, S.S. / McMullan, D. / McPhillips, T.M. / Acosta, C. / Canaves, J.M. / Elsliger, M.A. / Floyd, R. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Morse, A.T. / Quijano, K. / Spraggon, G. / van den Bedem, H. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJul 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN NI assigned based on electron density and coordination, potassium ion based on electron ...HETEROGEN NI assigned based on electron density and coordination, potassium ion based on electron density and environment.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4713
Polymers21,3741
Non-polymers982
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
hetero molecules

A: TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
hetero molecules

A: TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
hetero molecules

A: TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,88612
Polymers85,4954
Non-polymers3918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13050 Å2
ΔGint-105 kcal/mol
Surface area30020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.9566, 90.9566, 90.9566
Angle α, β, γ (deg.)90, 90, 90
Int Tables number195
Space group name H-MP23

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY


Mass: 21373.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1602 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1T8
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.2 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.8 M NaH2PO4/0.8 M KH2PO4, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.979105, 0.979445
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.9791051
30.9794451
ReflectionResolution: 2.3→40.677 Å / Num. obs: 11360 / % possible obs: 99.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 39.1 Å2 / Rsym value: 0.095 / Net I/σ(I): 18.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.324 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
SOLVEphasing
RESOLVEmodel building
CNS1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→40 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: POOR ELECTRON DENSITY (BROKEN 2FO-FC DENSITY AT THE 1 SIGMA LEVEL AND SOME NEGATIVE FO-FC DENSITY AT THE 3 SIGMA LEVEL) INDICATE THAT THE SIDECHAINS OF THE FOLLOWING RESIDUES MAY BE MORE ...Details: POOR ELECTRON DENSITY (BROKEN 2FO-FC DENSITY AT THE 1 SIGMA LEVEL AND SOME NEGATIVE FO-FC DENSITY AT THE 3 SIGMA LEVEL) INDICATE THAT THE SIDECHAINS OF THE FOLLOWING RESIDUES MAY BE MORE DISORDERED THAN INDICATED BY THEIR B-FACTORS: GLN-8, GLU-9, ARG-20, GLU-23, ARG-112, GLU- 136, GLU-156, AND GLU-173. NO ELECTRON DENSITY WAS OBSERVED FOR SIDECHAIN ATOMS BEYOND CB FOR LYS-134. THESE ATOMS WERE GIVEN AN OCCUPANCY OF ZERO.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 574 5 %RANDOM
Rwork0.19 ---
obs0.19 11136 99.9 %-
all-11409 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 34.42 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error6 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 2 97 1446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.2082
X-RAY DIFFRACTIONc_scbond_it2.712
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2693 48 4.9 %
Rwork0.2175 928 -

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