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- PDB-3e0y: The crystal structure of a conserved domain from a protein of Geo... -

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Basic information

Entry
Database: PDB / ID: 3e0y
TitleThe crystal structure of a conserved domain from a protein of Geobacter sulfurreducens PCA
ComponentsConserved domain protein
Keywordsstructural genomics / unknown function / APC87688.2 / conserved domain / Geobacter sulfurreducens PCA / PSI-2 / midwest center for structural genomics / MCSG / Protein Structure Initiative
Function / homologyGAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GAF domain protein, putative
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsTan, K. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved domain from a protein of Geobacter sulfurreducens PCA
Authors: Tan, K. / Bigelow, L. / Clancy, S. / Joachimiak, A.
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved domain protein
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7934
Polymers40,7472
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-35 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.421, 59.421, 223.175
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsauthors state that the biological assembly is experimentally unknown. The A and B chains are expected to form a dimer.

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Components

#1: Protein Conserved domain protein


Mass: 20373.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU1116 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q74E48
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15%(v/v) ethanol, 0.1M HEPES, 0.2M MgCl., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97959
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2007 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979591
ReflectionResolution: 3.1→42.3 Å / Num. all: 8896 / Num. obs: 8896 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 834 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→42.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.865 / SU B: 48.329 / SU ML: 0.395 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29089 418 4.7 %RANDOM
Rwork0.21649 ---
all0.21983 8419 --
obs0.21983 8419 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 3.1→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 2 0 2350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9653216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.585303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01124.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.80915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0151514
X-RAY DIFFRACTIONr_chiral_restr0.1230.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2850.21318
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21682
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.00421520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77832457
X-RAY DIFFRACTIONr_scbond_it0.9232867
X-RAY DIFFRACTIONr_scangle_it1.5053759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.103→3.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 27 -
Rwork0.29 567 -
obs-584 95.96 %
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)
15.9558-1.2174-0.90557.89950.95778.7723-0.3874-0.17260.34690.14620.23850.19190.1248-0.31210.14890.07860.1751-0.0262-0.1939-0.008-0.029747.99187.644489.6845
26.7801-1.1669-1.14176.81140.82046.75140.16860.0927-0.3092-0.1971-0.1796-0.30120.2062-0.29850.0110.05020.2472-0.029-0.0349-0.0132-0.009431.547933.632897.9082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA75 - 23811 - 174
2X-RAY DIFFRACTION2BB74 - 23810 - 174

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