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- PDB-3tj7: GBAA_1210 protein, a putative adenylate cyclase, from Bacillus an... -

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Basic information

Entry
Database: PDB / ID: 3tj7
TitleGBAA_1210 protein, a putative adenylate cyclase, from Bacillus anthracis in complex with AMP
ComponentsGBAA_1210 protein
KeywordsLYASE / structural genomics / Adenosine monophosphate / Center for Structural Genomics of Infectious Diseases / CSGID / CYTH-like superfamily / adenylate cyclase
Function / homology
Function and homology information


Uncharacterised protein family YjbK / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / CYTH domain-containing protein / CYTH domain-containing protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOsipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: GBAA_1210 protein, a putative adenylate cyclase, from Bacillus anthracis in complex with AMP
Authors: Osipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GBAA_1210 protein
B: GBAA_1210 protein
C: GBAA_1210 protein
D: GBAA_1210 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89718
Polymers90,8074
Non-polymers2,09014
Water4,216234
1
A: GBAA_1210 protein
B: GBAA_1210 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3127
Polymers45,4042
Non-polymers9095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-34 kcal/mol
Surface area17410 Å2
MethodPISA
2
C: GBAA_1210 protein
D: GBAA_1210 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58511
Polymers45,4042
Non-polymers1,1829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-52 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.229, 86.315, 76.438
Angle α, β, γ (deg.)90.000, 102.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GBAA_1210 protein


Mass: 22701.773 Da / Num. of mol.: 4 / Mutation: F43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS1117, BA_1210, GBAA_1210 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81TQ6, UniProt: A0A6L8P3N5*PLUS
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.8 M lithium sulfate, 0.1 M sodium acetate - HCl, pH 4.6, crystals were soaked in 10 mM AMP, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→37.4 Å / Num. all: 48611 / Num. obs: 48611 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.423 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.142.80.4592.0518880.92577.5
2.14-2.182.80.42422440.88190.9
2.18-2.223.10.40724130.9297.3
2.22-2.263.50.39424420.9298.6
2.26-2.313.80.3924760.9799.3
2.31-2.373.80.35724190.91299.3
2.37-2.423.80.29924370.95499.4
2.42-2.493.80.26624891.00299.4
2.49-2.563.80.21224531.04499.5
2.56-2.653.80.17824541.12499.6
2.65-2.743.80.17124931.15399.6
2.74-2.853.80.12924501.30299.7
2.85-2.983.80.10124771.3699.8
2.98-3.143.80.0824891.47599.8
3.14-3.333.80.06224761.60799.9
3.33-3.593.80.05324871.77999.9
3.59-3.953.80.04724961.877100
3.95-4.523.70.04825041.94999.8
4.52-5.73.70.04625012.19799.9
5.7-503.60.04625233.53798.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SY3

3sy3


Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.224 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2449 5 %RANDOM
Rwork0.1928 ---
all0.1955 48535 --
obs0.1955 48535 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 120.02 Å2 / Biso mean: 42.2101 Å2 / Biso min: 14.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å20.51 Å2
2--4.56 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 135 234 6034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226046
X-RAY DIFFRACTIONr_bond_other_d0.0020.023937
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9698208
X-RAY DIFFRACTIONr_angle_other_deg0.90639699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.29625.479303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.966151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7111519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021171
X-RAY DIFFRACTIONr_mcbond_it1.051.53590
X-RAY DIFFRACTIONr_mcbond_other0.2621.51444
X-RAY DIFFRACTIONr_mcangle_it1.95225833
X-RAY DIFFRACTIONr_scbond_it3.12532456
X-RAY DIFFRACTIONr_scangle_it5.0594.52359
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 149 -
Rwork0.281 2690 -
all-2839 -
obs-2839 78.34 %
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)
11.4876-0.21670.22441.0517-0.78860.8751-0.0409-0.07090.0803-0.03370.05160.01550.0471-0.0072-0.01070.01380.01470.01140.0462-0.01890.014131.012249.94647.9212
20.7360.6784-0.12871.18860.12130.2404-0.03990.2259-0.0683-0.02070.0942-0.0739-0.0391-0.0732-0.05430.0196-0.00440.01940.0951-0.03510.04750.67739.206634.5097
31.5776-1.1050.4911.131-0.43571.11240.05560.02310.0084-0.0245-0.021-0.05860.093-0.1525-0.03460.0506-0.06270.02020.04540.0030.017474.547638.319712.6857
41.16360.3195-0.28150.88960.82083.08330.0869-0.12140.1862-0.1979-0.03110.2842-0.2930.3032-0.05580.0523-0.03190.02830.08980.00570.080489.608249.2672-5.8501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 175
2X-RAY DIFFRACTION1A501 - 609
3X-RAY DIFFRACTION1A193 - 254
4X-RAY DIFFRACTION2B0 - 175
5X-RAY DIFFRACTION2B501
6X-RAY DIFFRACTION2B193 - 274
7X-RAY DIFFRACTION3C0 - 176
8X-RAY DIFFRACTION3C501 - 610
9X-RAY DIFFRACTION3C193 - 242
10X-RAY DIFFRACTION4D-1 - 174
11X-RAY DIFFRACTION4D501 - 605
12X-RAY DIFFRACTION4D193 - 234

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