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- PDB-1oz9: Crystal structure of AQ_1354, a hypothetical protein from Aquifex... -

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Basic information

Entry
Database: PDB / ID: 1oz9
TitleCrystal structure of AQ_1354, a hypothetical protein from Aquifex aeolicus
ComponentsHypothetical protein AQ_1354
KeywordsUNKNOWN FUNCTION / matrix metalloproteinase type fold / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


RNA endonuclease activity / metalloendopeptidase activity / rRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / cytoplasm
Similarity search - Function
Metalloproteases ("zincins"), catalytic domain / Endoribonuclease YbeY, conserved site / Uncharacterized protein family UPF0054 signature. / Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease YbeY
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.894 Å
AuthorsOganesyan, V. / Busso, D. / Brandsen, J. / Chen, S. / Jancarik, J. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus.
Authors: Oganesyan, V. / Busso, D. / Brandsen, J. / Chen, S. / Jancarik, J. / Kim, R. / Kim, S.H.
History
DepositionApr 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein AQ_1354


Theoretical massNumber of molelcules
Total (without water)17,3721
Polymers17,3721
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.018, 58.018, 110.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a monomer

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Components

#1: Protein Hypothetical protein AQ_1354


Mass: 17372.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O67367
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.76 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4K, Na Acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
220 mMTris-HCl1droppH7.0
310 mM1dropNaCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
6200 mMsodium acetate1reservoir
7100 mMTris-HCl1reservoirpH8.5
830 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→41.17 Å / Num. all: 14413 / Num. obs: 14413 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 25
Reflection shellResolution: 1.894→1.943 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.2 / Num. unique all: 982 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 41.2 Å / Num. obs: 28054 / % possible obs: 96.3 % / Redundancy: 9.3 %
Reflection shell
*PLUS
Highest resolution: 1.89 Å / Lowest resolution: 1.97 Å / % possible obs: 85.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.25

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.894→12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.105 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23423 712 5 %RANDOM
Rwork0.20524 ---
all0.21522 ---
obs0.20658 13420 100 %-
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: 22.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.133 Å0.146 Å
Refinement stepCycle: LAST / Resolution: 1.894→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 0 50 1201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211166
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9871558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5983140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.53415247
X-RAY DIFFRACTIONr_chiral_restr0.1060.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02844
X-RAY DIFFRACTIONr_nbd_refined0.2130.3479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.583
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5320.520
X-RAY DIFFRACTIONr_mcbond_it0.7811.5696
X-RAY DIFFRACTIONr_mcangle_it1.50421119
X-RAY DIFFRACTIONr_scbond_it2.6553470
X-RAY DIFFRACTIONr_scangle_it4.5274.5439
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 48 -
Rwork0.22 939 -
obs-982 82 %
Refinement TLS params.Method: refined / Origin x: 47.99 Å / Origin y: 18.021 Å / Origin z: 43.601 Å
111213212223313233
T0.1014 Å2-0.0123 Å2-0.0396 Å2-0.0064 Å2-0.0086 Å2--0.0522 Å2
L2.8889 °2-0.7968 °21.4808 °2-3.9555 °2-0.2594 °2--3.0802 °2
S0.0887 Å °-0.0857 Å °0.0419 Å °0.1687 Å °-0.0634 Å °-0.2591 Å °0.0133 Å °0.1127 Å °-0.0253 Å °
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.89 Å / Num. reflection obs: 15227 / % reflection Rfree: 5 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.524

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