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- PDB-1xrx: Crystal structure of a DNA-binding protein -

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Basic information

Entry
Database: PDB / ID: 1xrx
TitleCrystal structure of a DNA-binding protein
ComponentsSeqA protein
KeywordsREPLICATION INHIBITOR / Protein filament / Left-handed helix / DNA replication inhibitor
Function / homology
Function and homology information


SeqA-DNA complex / nucleoid organization / double-stranded methylated DNA binding / hemi-methylated DNA-binding / sister chromatid cohesion / DNA replication origin binding / negative regulation of DNA-templated DNA replication initiation / response to radiation / regulation of DNA-templated transcription / protein homodimerization activity ...SeqA-DNA complex / nucleoid organization / double-stranded methylated DNA binding / hemi-methylated DNA-binding / sister chromatid cohesion / DNA replication origin binding / negative regulation of DNA-templated DNA replication initiation / response to radiation / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Negative modulator of initiation of replication SeqA / Replication modulator SeqA, C-terminal DNA-binding domain / Negative modulator of initiation of replication SeqA, N-terminal / Replication modulator SeqA, C-terminal DNA-binding domain superfamily / SeqA protein C-terminal domain / SeqA protein N-terminal domain / Arc-type ribbon-helix-helix / Ribbon-helix-helix
Similarity search - Domain/homology
Negative modulator of initiation of replication / Negative modulator of initiation of replication
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsGuarne, A. / Brendler, T. / Zhao, Q. / Ghirlando, R. / Austin, S. / Yang, W.
CitationJournal: Embo J. / Year: 2005
Title: Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization.
Authors: Guarne, A. / Brendler, T. / Zhao, Q. / Ghirlando, R. / Austin, S. / Yang, W.
History
DepositionOct 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 6, 2013Group: Other
Remark 295NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON- ...NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 50 C 1 .. 50 M 2 B 1 .. 50 D 1 .. 50 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS (2 DIMERS). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The asymmetric unit contains two dimers that form a linear polymer representing the known biologically significant oligomerization state of the molecule by applying the non-crystallographic and crystallographic operations given in remarks 295 and 350 and the MTRIX records below.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SeqA protein
B: SeqA protein
C: SeqA protein
D: SeqA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8215
Polymers22,7814
Non-polymers401
Water3,153175
1
A: SeqA protein
B: SeqA protein
C: SeqA protein
D: SeqA protein
hetero molecules

A: SeqA protein
B: SeqA protein
C: SeqA protein
D: SeqA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,64210
Polymers45,5618
Non-polymers802
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546y,x-1,-z+11
2
A: SeqA protein
B: SeqA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4303
Polymers11,3902
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SeqA protein
D: SeqA protein


Theoretical massNumber of molelcules
Total (without water)11,3902
Polymers11,3902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.179, 112.179, 62.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-98-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2795, 0.4208, -0.863), (0.4287, 0.7496, 0.5043), (0.8591, -0.511, 0.0292)
Vector: 81.1193, -15.3445, -17.4673)
DetailsStructural Assembly: dimer. Two monomers are related by a dyad axis. The a.s.u. contains two of these dimers (AB and CD molecules) / Biological Assembly: filament. Adjacent dimers are related by a dyad axis (perpendicular to the filament) and a four-fold screw axis (parallel to the filament axis)

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Components

#1: Protein/peptide
SeqA protein


Mass: 5695.182 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: seqA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P36658, UniProt: P0AFY8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 5.04 Å3/Da / Density % sol: 75.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD, calcium chloride, TRIS, isopropanol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X9B10.97938, 0.96859, 0.98241
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMar 4, 2003
RIGAKU RAXIS2IMAGE PLATEMar 24, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Two Si crystalsMADMx-ray1
2Yale mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.968591
30.982411
41.54181
ReflectionResolution: 2.15→25 Å / Num. all: 24769 / Num. obs: 24398 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.054 / Net I/σ(I): 26.1
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1200 / Rsym value: 0.411 / % possible all: 84.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→24.71 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1242499.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1665 6.8 %RANDOM
Rwork0.222 ---
all0.223 24736 --
obs-24365 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1499 Å2 / ksol: 0.346944 e/Å3
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.23 Å2-2.74 Å20 Å2
2---10.23 Å20 Å2
3---20.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-25 Å
Luzzati sigma a0.5 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.15→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 1 175 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.61
X-RAY DIFFRACTIONc_mcbond_it3.691.5
X-RAY DIFFRACTIONc_mcangle_it5.282
X-RAY DIFFRACTIONc_scbond_it6.192
X-RAY DIFFRACTIONc_scangle_it8.082.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.475 254 6.8 %
Rwork0.438 3491 -
obs-3001 91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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