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- PDB-2ehp: Crystal Structure of a Putative protein (AQ1627) from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2ehp
TitleCrystal Structure of a Putative protein (AQ1627) from Aquifex aeolicus
Componentsaq_1627 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative protein / Aquifex aeolicus / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyAlpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein aq_1627
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsKumarevel, T.S. / Karthe, P. / Nakano, N. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of a Putative protein (AQ1627) from Aquifex aeolicus
Authors: Kumarevel, T.S. / Karthe, P. / Nakano, N. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aq_1627 protein
B: aq_1627 protein


Theoretical massNumber of molelcules
Total (without water)27,6412
Polymers27,6412
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-20 kcal/mol
Surface area10970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.353, 53.873, 60.168
Angle α, β, γ (deg.)90.00, 96.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

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Components

#1: Protein aq_1627 protein


Mass: 13820.679 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O67549
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40% Ethanol, 5% PEG1000, Phosphate-Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97884, 0.9000, 0.97973
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 28, 2006 / Details: Si
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.91
30.979731
ReflectionResolution: 1.3→50 Å / Num. all: 51115 / Num. obs: 51115 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.034
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.204 / Num. unique all: 4884 / % possible all: 85.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1028214.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2564 5 %RANDOM
Rwork0.227 ---
obs0.227 51106 89 %-
all-51115 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1226 Å2 / ksol: 0.347829 e/Å3
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å2-2.4 Å2
2---1.71 Å20 Å2
3----2.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 0 150 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 411 5.1 %
Rwork0.242 7662 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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