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- PDB-5a1q: Crystal structure of Archaeoglobus fulgidus Af1502 -

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Basic information

Entry
Database: PDB / ID: 5a1q
TitleCrystal structure of Archaeoglobus fulgidus Af1502
ComponentsAF1502
KeywordsUNKNOWN FUNCTION / STAC / STAC DOMAIN
Function / homologyUncharacterized protein AF_1502
Function and homology information
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsAlbrecht, R. / Lupas, A.N. / Hartmann, M.D.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Stac-A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems.
Authors: Korycinski, M. / Albrecht, R. / Ursinus, A. / Hartmann, M.D. / Coles, M. / Martin, J. / Dunin-Horkawicz, S. / Lupas, A.N.
History
DepositionMay 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AF1502
B: AF1502
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9873
Polymers16,8912
Non-polymers961
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-18.5 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.500, 56.720, 62.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AF1502


Mass: 8445.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O28770
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 170 MM AMMONIUM SULFATE, 25.5 %(W/V) PEG 4000, 15 %(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→35.2 Å / Num. obs: 20859 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.65
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.62 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.07 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→35.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.626 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21637 1065 5.1 %RANDOM
Rwork0.17416 ---
obs0.17633 19701 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.675 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--0.98 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 5 116 1240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021194
X-RAY DIFFRACTIONr_bond_other_d0.0010.021185
X-RAY DIFFRACTIONr_angle_refined_deg1.9522.0451616
X-RAY DIFFRACTIONr_angle_other_deg0.94332769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7155157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21926.60756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5115239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.553154
X-RAY DIFFRACTIONr_chiral_restr0.1280.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5426.561568
X-RAY DIFFRACTIONr_mcbond_other3.5526.526567
X-RAY DIFFRACTIONr_mcangle_it4.29910.939712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.0869.492626
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.596→1.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 63 -
Rwork0.257 1374 -
obs--93.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.81990.9510.53292.9558-0.78782.62750.0644-0.2524-0.33140.1829-0.0454-0.03410.21930.0992-0.0190.06240.01320.00730.02620.02760.043531.254629.76368.9598
23.95110.779-1.16643.8158-0.35242.2035-0.0156-0.15620.22630.1515-0.01570.1395-0.1605-0.11230.03130.04460.0137-0.00780.0197-0.01710.021132.308352.35715.9351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 68
2X-RAY DIFFRACTION2B0 - 67

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