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

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Basic information

Entry
Database: PDB / ID: 2eiu
TitleCrystal Structure of a Putative protein (AQ1627) from Aquifex aeolicus
ComponentsHypothetical protein aq_1627
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 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 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein aq_1627
C: Hypothetical protein aq_1627
D: Hypothetical protein aq_1627
E: Hypothetical protein aq_1627
F: Hypothetical protein aq_1627
G: Hypothetical protein aq_1627


Theoretical massNumber of molelcules
Total (without water)82,3616
Polymers82,3616
Non-polymers00
Water4,306239
1
A: Hypothetical protein aq_1627
F: Hypothetical protein aq_1627


Theoretical massNumber of molelcules
Total (without water)27,4542
Polymers27,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-20 kcal/mol
Surface area11190 Å2
MethodPISA, PQS
2
C: Hypothetical protein aq_1627
E: Hypothetical protein aq_1627


Theoretical massNumber of molelcules
Total (without water)27,4542
Polymers27,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-20 kcal/mol
Surface area11280 Å2
MethodPISA, PQS
3
D: Hypothetical protein aq_1627
G: Hypothetical protein aq_1627


Theoretical massNumber of molelcules
Total (without water)27,4542
Polymers27,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-19 kcal/mol
Surface area11110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.022, 174.092, 58.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Hypothetical protein aq_1627


Mass: 13726.889 Da / Num. of mol.: 6
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.: 239 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.2M Magnesium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 28, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 50865 / Num. obs: 50865 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2→2.07 Å / Redundancy: 8 % / Rmerge(I) obs: 0.335 / Num. unique all: 5093 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EHP

2ehp


Resolution: 2→19.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 120757.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2526 5.1 %RANDOM
Rwork0.23 ---
all0.23 50865 --
obs0.23 50003 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2297 Å2 / ksol: 0.35556 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--4.1 Å20 Å2
3----2.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5585 0 0 239 5824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 389 4.9 %
Rwork0.257 7491 -
obs--92.1 %
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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