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- PDB-2b1d: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' Methionine Repressor... -

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Basic information

Entry
Database: PDB / ID: 2b1d
Title5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' Methionine Repressor binding site
Components5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
KeywordsDNA / sequence dependent DNA deformability / protein-DNA recognition
Function / homologyCOBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBerman, H.M. / Locasale, J.W. / Napoli, A.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Signatures of protein-DNA recognition in free DNA binding sites.
Authors: Locasale, J.W. / Napoli, A.A. / Chen, S. / Berman, H.M. / Lawson, C.L.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
C: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
D: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
E: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
F: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,48810
Polymers21,9806
Non-polymers5084
Water1,00956
1
A: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5124
Polymers7,3272
Non-polymers1852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
D: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4883
Polymers7,3272
Non-polymers1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
F: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4883
Polymers7,3272
Non-polymers1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.980, 40.346, 40.255
Angle α, β, γ (deg.)82.15, 69.13, 81.44
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'


Mass: 3663.392 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, sodium cacodylate, cobalt hexamine, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3cobalt hexamine11
4magnesium chloride11
5H2O11
6MPD12
7sodium cacodylate12
8cobalt hexamine12
9magnesium chloride12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1004 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1004 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 7790 / Num. obs: 7790 / % possible obs: 97.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.483
Reflection shellResolution: 2.5→2.57 Å / % possible obs: 97.6 % / Rmerge(I) obs: 0.199 / Num. measured obs: 614 / Χ2: 1.936 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ID BD0001 (PDB ID 423D)

423d


Resolution: 2.5→39.84 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.384 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.787 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.284 624 8.1 %RANDOM
Rwork0.235 ---
all0.239 7684 --
obs0.239 7684 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0.63 Å2-2.49 Å2
2---0.51 Å20.23 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1458 22 56 1536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211656
X-RAY DIFFRACTIONr_angle_refined_deg7.66132568
X-RAY DIFFRACTIONr_chiral_restr0.1320.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0490.02766
X-RAY DIFFRACTIONr_nbd_refined0.2280.2615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.350.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.255
X-RAY DIFFRACTIONr_scbond_it8.55131656
X-RAY DIFFRACTIONr_scangle_it12.3964.52568
LS refinement shellResolution: 2.5→2.885 Å / Total num. of bins used: 4 /
RfactorNum. reflection
Rfree0.535 203
Rwork0.442 2468
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)
11.45940.68640.97260.11320.04954.26280.21730.1279-0.0979-0.09370.0663-0.03690.470.1208-0.28350.30080.0685-0.0510.1786-0.00430.067-38.1293-23.765327.8991
23.40590.27680.0540.9713-0.05730.645-0.03880.24070.43420.01120.009-0.13880.05870.02940.02970.09020.02920.03140.18520.07730.2189-33.281-8.05430.4043
30.86771.06280.0356.9103-0.04841.28680.0270.02430.1806-0.0404-0.12750.3281-0.0751-0.04930.10050.2498-0.01030.01970.0004-0.00110.1975-46.9346-9.129646.0194
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Label seq-ID: 1 - 12

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-ID
11AA1 - 12
21BB13 - 24
32CC1 - 12
42DD13 - 24
53EE1 - 12
63FF13 - 24

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