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- PDB-2p6c: Crystal structure of hypothetical protein aq_2013 from Aquifex ae... -

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Basic information

Entry
Database: PDB / ID: 2p6c
TitleCrystal structure of hypothetical protein aq_2013 from Aquifex aeolicus VF5.
Componentsaq_2013 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyYjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / UPF0047 protein YjbQ-like / Jelly Rolls / Sandwich / Mainly Beta / PHOSPHATE ION / YjbQ family protein
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein aq_2013 from Aquifex aeolicus VF5
Authors: Yamamoto, H. / Kunishima, N.
History
DepositionMar 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 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: aq_2013 protein
B: aq_2013 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5948
Polymers32,0252
Non-polymers5706
Water4,522251
1
A: aq_2013 protein
hetero molecules

A: aq_2013 protein
hetero molecules

A: aq_2013 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,89212
Polymers48,0373
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10200 Å2
ΔGint-116 kcal/mol
Surface area15900 Å2
MethodPISA, PQS
2
B: aq_2013 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2974
Polymers16,0121
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: aq_2013 protein
hetero molecules

B: aq_2013 protein
hetero molecules

B: aq_2013 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,89212
Polymers48,0373
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.248, 70.248, 133.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1113-

HOH

21A-1114-

HOH

31B-1096-

HOH

41B-1097-

HOH

DetailsThe biological assembly is a trimer.

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Components

#1: Protein aq_2013 protein


Mass: 16012.288 Da / Num. of mol.: 2
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-CodonPlus(DE3)-RIL / References: UniProt: O67812
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.6
Details: 0.1M Sodium Citrate, 1.0M Ammonium dihydrogen Phosphate, pH 5.6, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 16682 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 16.729 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.045 / Net I/σ(I): 32.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 15 / Num. unique all: 1660 / Rsym value: 0.093 / % possible all: 100

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Processing

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

1vmj


Resolution: 2→35.12 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THOUGEOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 816 -RANDOM
Rwork0.183 ---
obs0.183 16647 99.9 %-
all-16663 --
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20.73 Å20 Å2
2---0.33 Å20 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 30 251 2537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d1.37
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.238 137 -
Rwork0.2 --
obs-2775 100 %

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