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- PDB-2e8e: Crystal Structure of a hypothetical protein (Aq_1549) from Aquife... -

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Basic information

Entry
Database: PDB / ID: 2e8e
TitleCrystal Structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5 (Reduced form)
ComponentsHypothetical protein Aq_1549
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Aq_1549 / Osmatically induced protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / OsmC family peroxiredoxin
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5
Authors: Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJan 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Aq_1549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1922
Polymers15,0381
Non-polymers1541
Water1,63991
1
A: Hypothetical protein Aq_1549
hetero molecules

A: Hypothetical protein Aq_1549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3844
Polymers30,0752
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7090 Å2
ΔGint-60 kcal/mol
Surface area11950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.516, 65.516, 59.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Hypothetical protein Aq_1549


Mass: 15037.618 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codonplus-RIL-X / References: UniProt: O67503
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 50% PEG 200, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2006 / Details: Si
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 14883 / Num. obs: 14883 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.367 / Num. unique all: 1450 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E8C

2e8c


Resolution: 1.7→19.58 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1124848.21 / 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
Rfree0.233 743 5 %RANDOM
Rwork0.209 ---
obs0.209 14837 99.6 %-
all-14883 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.5113 Å2 / ksol: 0.397908 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 8 91 1152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 123 5.1 %
Rwork0.26 2273 -
obs--98.6 %
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.param
X-RAY DIFFRACTION4ion.paramion.param
X-RAY DIFFRACTION5DTT.paramDTT.top

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