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- PDB-3sy3: GBAA_1210 protein, a putative adenylate cyclase, from Bacillus an... -

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Basic information

Entry
Database: PDB / ID: 3sy3
TitleGBAA_1210 protein, a putative adenylate cyclase, from Bacillus anthracis
ComponentsGBAA_1210 protein
KeywordsLYASE / structural genomics / 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
PHOSPHATE ION / CYTH domain-containing protein / CYTH domain-containing protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 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.
Authors: Osipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)91,75714
Polymers90,8074
Non-polymers95010
Water3,117173
1
A: GBAA_1210 protein
B: GBAA_1210 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7836
Polymers45,4042
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-33 kcal/mol
Surface area17780 Å2
MethodPISA
2
C: GBAA_1210 protein
D: GBAA_1210 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9738
Polymers45,4042
Non-polymers5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-47 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.322, 85.997, 76.513
Angle α, β, γ (deg.)90.000, 102.120, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1 M phosphate buffer, chymotrypsin, pH 5.0, 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: Jun 17, 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: 2.14→37.3 Å / Num. all: 46815 / Num. obs: 46815 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.817 / 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
2.14-2.182.90.5242.1622281.06195.1
2.18-2.223.20.51722851.0298
2.22-2.263.40.49723451.11499.5
2.26-2.313.60.4823381.075100
2.31-2.363.80.4623091100
2.36-2.413.80.44223491.096100
2.41-2.473.90.39323401.148100
2.47-2.5440.31623661.147100
2.54-2.6140.27123451.208100
2.61-2.740.23523431.309100
2.7-2.7940.20623521.368100
2.79-2.940.1523201.457100
2.9-3.0440.12423611.594100
3.04-3.240.09423821.84100
3.2-3.440.07223102.11799.9
3.4-3.663.90.06423692.59899.8
3.66-4.033.90.05923573.11199.8
4.03-4.613.80.05523483.5499.7
4.61-5.813.60.0523633.54299.6
5.81-503.40.04724053.81298.6

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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
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→37.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.89 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 2332 5 %RANDOM
Rwork0.1962 ---
all0.1988 46743 --
obs0.1988 46743 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 133.61 Å2 / Biso mean: 44.7822 Å2 / Biso min: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20.66 Å2
2--4.27 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.14→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5652 0 50 173 5875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225886
X-RAY DIFFRACTIONr_bond_other_d0.0010.023852
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9547977
X-RAY DIFFRACTIONr_angle_other_deg0.87339492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.22925.541296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.146151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6761517
X-RAY DIFFRACTIONr_chiral_restr0.0930.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021128
X-RAY DIFFRACTIONr_mcbond_it0.8621.53536
X-RAY DIFFRACTIONr_mcbond_other0.1991.51432
X-RAY DIFFRACTIONr_mcangle_it1.65825756
X-RAY DIFFRACTIONr_scbond_it2.75432350
X-RAY DIFFRACTIONr_scangle_it4.6094.52209
LS refinement shellResolution: 2.139→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 139 -
Rwork0.284 3030 -
all-3169 -
obs-3469 91.59 %
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)
12.3418-0.28610.28930.8266-0.45120.4267-0.039-0.14080.0747-0.0060.00270.04920.0567-0.010.03630.02580.02040.01520.0562-0.00850.028430.849349.647847.8789
21.13410.6238-0.2351.3444-0.03840.5989-0.02560.1966-0.0393-0.09010.0861-0.0652-0.0157-0.1098-0.06050.02080.00750.00010.0485-0.00470.036750.676238.924334.3024
31.5296-1.4682-0.19881.6089-0.01420.7878-0.0086-0.04420.08810.09480.0401-0.0596-0.0134-0.159-0.03150.0711-0.03930.01110.07020.00830.030974.84138.375212.9608
43.3425-0.8102-0.12570.9070.01964.04520.0145-0.24630.62780.0602-0.0086-0.0937-0.65860.4746-0.00580.1458-0.07340.02670.13640.00120.172890.131149.1987-5.7546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 175
2X-RAY DIFFRACTION1A193 - 239
3X-RAY DIFFRACTION2B0 - 174
4X-RAY DIFFRACTION2B193 - 251
5X-RAY DIFFRACTION3C0 - 176
6X-RAY DIFFRACTION3C193 - 232
7X-RAY DIFFRACTION4D-1 - 174
8X-RAY DIFFRACTION4D193 - 219

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