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- PDB-2rkh: Crystal structure of a putative AphA-like transcription factor (Z... -

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Basic information

Entry
Database: PDB / ID: 2rkh
TitleCrystal structure of a putative AphA-like transcription factor (ZP_00208345.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution
ComponentsPutative AphA-like transcription factor
KeywordsTRANSCRIPTION / ZP_00208345.1 / Putative AphA-like Transcription Factor / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyHscB, C-terminal domain / Monooxygenase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative AphA-like transcription factor (ZP_00208345.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. 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. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00208345.1.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative AphA-like transcription factor


Theoretical massNumber of molelcules
Total (without water)20,1111
Polymers20,1111
Non-polymers00
Water1,02757
1
A: Putative AphA-like transcription factor

A: Putative AphA-like transcription factor


Theoretical massNumber of molelcules
Total (without water)40,2212
Polymers40,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.620, 66.620, 92.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsTHE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING.

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Components

#1: Protein Putative AphA-like transcription factor


Mass: 20110.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Strain: MS-1 / Gene: ZP_00208345.1 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 15.0% Glycerol, 0.17M NaOAc, 25.5% PEG 4000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9795, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97971
ReflectionResolution: 2→28.364 Å / Num. obs: 14688 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.566 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.26
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.665294952578197.4
2.07-2.150.4732.9985726131100
2.15-2.250.3354.11045127541100
2.25-2.370.2265.91042427401100
2.37-2.520.1568.51028526971100
2.52-2.710.10212.41008326451100
2.71-2.990.06418.4105722771199.9
2.99-3.420.04126.81016526631100
3.42-4.30.02937.8101282689199.9
4.3-28.3640.02342.9102082724199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28.364 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.358 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RAMACHANDRAN OUTLIER RESIDUE 100 LIES IN A POORLY ORDERED REGION. 5. THERE IS SOME UNIDENTIFIED DENSITY NEAR RESIDUE 37.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 736 5 %RANDOM
Rwork0.212 ---
obs0.214 14640 99.79 %-
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: 39.306 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→28.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 57 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211253
X-RAY DIFFRACTIONr_bond_other_d0.0030.02851
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9981697
X-RAY DIFFRACTIONr_angle_other_deg1.34132069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6085168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.3821.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60515220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1181514
X-RAY DIFFRACTIONr_chiral_restr0.080.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021396
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
X-RAY DIFFRACTIONr_nbd_refined0.1870.2253
X-RAY DIFFRACTIONr_nbd_other0.1250.2782
X-RAY DIFFRACTIONr_nbtor_refined0.1390.2620
X-RAY DIFFRACTIONr_nbtor_other0.0740.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.26
X-RAY DIFFRACTIONr_mcbond_it2.0353967
X-RAY DIFFRACTIONr_mcbond_other0.3923340
X-RAY DIFFRACTIONr_mcangle_it2.62151292
X-RAY DIFFRACTIONr_scbond_it4.3268458
X-RAY DIFFRACTIONr_scangle_it5.75811401
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 51 -
Rwork0.263 974 -
all-1025 -
obs--98.37 %
Refinement TLS params.Method: refined / Origin x: 17.74 Å / Origin y: 16.563 Å / Origin z: 8.679 Å
111213212223313233
T-0.1713 Å2-0.0007 Å20.0144 Å2--0.1163 Å20.0372 Å2---0.0953 Å2
L2.1808 °20.272 °20.5678 °2-2.2507 °2-1.0641 °2--3.6268 °2
S0.0816 Å °-0.334 Å °-0.4478 Å °0.0246 Å °0.016 Å °0.1797 Å °0.2893 Å °-0.2128 Å °-0.0976 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 667 - 67
2X-RAY DIFFRACTION1AA75 - 14576 - 146
3X-RAY DIFFRACTION1AA148 - 179149 - 180

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