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- PDB-1lfp: Crystal Structure of a Conserved Hypothetical Protein Aq1575 from... -

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Basic information

Entry
Database: PDB / ID: 1lfp
TitleCrystal Structure of a Conserved Hypothetical Protein Aq1575 from Aquifex Aeolicus
ComponentsHypothetical protein AQ_1575
KeywordsRNA BINDING PROTEIN / Hypothetical / New fold / thermostability / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
YebC, transcriptional regulation domain / Transcriptional regulator TACO1-like / Transcriptional regulator TACO1-like, domain 3 / : / : / TACO1/YebC second and third domain / TACO1/YebC protein N-terminal domain / YebC-like / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal ...YebC, transcriptional regulation domain / Transcriptional regulator TACO1-like / Transcriptional regulator TACO1-like, domain 3 / : / : / TACO1/YebC second and third domain / TACO1/YebC protein N-terminal domain / YebC-like / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable transcriptional regulatory protein aq_1575
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsShin, D.H. / Yokota, H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus.
Authors: Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionApr 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein AQ_1575


Theoretical massNumber of molelcules
Total (without water)28,0401
Polymers28,0401
Non-polymers00
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.790, 65.350, 73.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein AQ_1575


Mass: 28040.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67517
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG3350, 0.2M Ammonium Nitrate, 10 mM NAD, 3% PEG400, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 21.5-22.5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
225 mMTris-HCl1droppH6.8
3110 mM1dropNaCl
410 %PEG33501drop
50.1 Mammonium nitrate1drop
65 mMNAD1drop
71.5 %PEG4001drop
820 %PEG33501reservoir
90.2 Mammonium nitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97864 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2002
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 1.72→36.2 Å / Num. obs: 22781 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.9 Å2
Reflection shellResolution: 1.72→1.73 Å / % possible all: 48
Reflection
*PLUS
Highest resolution: 1.71 Å / Num. obs: 42899 / % possible obs: 96 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.71 Å / % possible obs: 48.2 % / Redundancy: 5 % / Num. unique obs: 1081 / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.72→29.88 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 410192.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2045 10 %RANDOM
Rwork0.228 ---
all0.23 22781 --
obs0.23 20481 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9766 Å2 / ksol: 0.297912 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.44 Å20 Å20 Å2
2---3.54 Å20 Å2
3---9.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.72→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 350 2275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 1.72→1.82 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 222 9.7 %
Rwork0.215 2056 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.71 Å / Lowest resolution: 20 Å / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.99
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Highest resolution: 1.71 Å / Lowest resolution: 1.73 Å / Rfactor obs: 0.215

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