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- PDB-1xm7: The Crystal Structure of the Protein of Unknown Function AQ665 fr... -

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Basic information

Entry
Database: PDB / ID: 1xm7
TitleThe Crystal Structure of the Protein of Unknown Function AQ665 from Aquifex aeolicus
Componentshypothetical protein aq_1665
KeywordsStructural genomics / unknown function / protein_aq1665 / protein structure initiative / midwest center for structural genomics / PSI / MCSG
Function / homology
Function and homology information


Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Calcineurin-like phosphoesterase domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsZhang, R. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the hypothetical protein aq_1665 from Aquifex aeolicus
Authors: Zhang, R. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Nov 13, 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_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein aq_1665
B: hypothetical protein aq_1665


Theoretical massNumber of molelcules
Total (without water)47,3742
Polymers47,3742
Non-polymers00
Water1,26170
1
A: hypothetical protein aq_1665


Theoretical massNumber of molelcules
Total (without water)23,6871
Polymers23,6871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein aq_1665


Theoretical massNumber of molelcules
Total (without water)23,6871
Polymers23,6871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.582, 94.596, 67.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein existed as monomer.MolA and MolB represent two molecules in the asymmetric unit.

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Components

#1: Protein hypothetical protein aq_1665


Mass: 23687.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O67582
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.05 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis/Tris Propane, 2.8M Sodium Acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.9465
DetectorType: SBC-2 / Detector: CCD / Date: Oct 26, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.94651
ReflectionResolution: 2.4→40 Å / Num. all: 22228 / Num. obs: 21851 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.92
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2186 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 262072.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1849 5 %RANDOM
Rwork0.209 ---
all0.22 40712 --
obs0.209 36804 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4573 Å2 / ksol: 0.344659 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å20 Å2
2---3.33 Å20 Å2
3----4.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 0 70 3260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 251 5.2 %
Rwork0.346 4572 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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