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- PDB-9ovi: Crystal Structure of SH3-like_bac-type domain (79-145) of Conserv... -

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Basic information

Entry
Database: PDB / ID: 9ovi
TitleCrystal Structure of SH3-like_bac-type domain (79-145) of Conserved domain protein GBAA_2967 from Bacillus anthracis Ames ancestor
ComponentsConserved domain protein
KeywordsUNKNOWN FUNCTION / SH3b domain / cell wall binding protein with conserved domain / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / 3D domain / 3D domain / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / RlpA-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Conserved domain protein
Similarity search - Component
Biological speciesBacillus anthracis str. Ames (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Dubrovska, I. / Winsor, J. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal Structure of SH3-like_bac-type domain (79-145) of Conserved domain protein GBAA_2967 from Bacillus anthracis Ames ancestor.
Authors: Minasov, G. / Dubrovska, I. / Winsor, J. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionMay 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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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)15,5688
Polymers15,3352
Non-polymers2336
Water3,441191
1
A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8305
Polymers7,6681
Non-polymers1624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7383
Polymers7,6681
Non-polymers702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.281, 50.276, 84.602
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 Conserved domain protein


Mass: 7667.573 Da / Num. of mol.: 2 / Fragment: residues 79-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria)
Strain: Ames ancestor / Gene: GBAA_2967 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: A0A6L7HMQ8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.6 Å3/Da / Density meas: 52.7 Mg/m3 / Density % sol: 51.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 6.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG3350; Cryo: Reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 25567 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.081 / Rsym value: 0.075 / Χ2: 1.013 / Net I/σ(I): 24.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1153 / CC1/2: 0.714 / CC star: 0.913 / Rpim(I) all: 0.394 / Rrim(I) all: 0.949 / Rsym value: 0.859 / Χ2: 0.999 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.42 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.458 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18385 1319 5.2 %RANDOM
Rwork0.16448 ---
obs0.16548 24144 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2---1.11 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 14 191 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161110
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.841569
X-RAY DIFFRACTIONr_angle_other_deg0.4561.8072566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.85455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.02210223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021379
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02269
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_it1.050.905564
X-RAY DIFFRACTIONr_mcbond_other1.0490.912565
X-RAY DIFFRACTIONr_mcangle_it1.7711.62712
X-RAY DIFFRACTIONr_mcangle_other1.771.619713
X-RAY DIFFRACTIONr_scbond_it2.1281.226600
X-RAY DIFFRACTIONr_scbond_other2.0951.192593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2972.078858
X-RAY DIFFRACTIONr_long_range_B_refined7.05914.741339
X-RAY DIFFRACTIONr_long_range_B_other6.60812.221265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 101 -
Rwork0.265 1698 -
obs--97.98 %
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)
17.6272-3.2992.84115.2694-1.26977.69190.191-0.02220.2606-0.1683-0.00970.0852-0.4356-0.2237-0.18130.09570.02330.03830.00860.01240.054-21.8320.4114-15.855
22.43451.44510.90363.014-0.12351.72510.0352-0.08570.14020.1679-0.026-0.0178-0.0286-0.0848-0.00920.02940.00680.00780.0081-0.00190.047-13.86772.38273.5531
32.86752.4499-1.50413.7845-4.59277.2843-0.03510.0007-0.0427-0.11530.0034-0.04020.1386-0.00040.03180.0827-0.0050.01220.0013-0.00640.0346-18.3942-1.7328-5.4757
46.3985-3.0773-0.27613.8509-0.05121.40850.02180.19010.1453-0.1919-0.0524-0.0215-0.07540.06370.03050.0222-0.00770.00110.01050.00570.0541-12.19345.921-5.054
51.48030.9110.6862.16720.72850.6026-0.0310.1167-0.0098-0.12780.0989-0.1386-0.00040.0481-0.06790.0464-0.00110.01360.02310.00160.0485-11.533-0.9255-4.2172
613.67424.55661.59655.31680.08068.8776-0.15250.5814-0.2674-0.7120.1179-0.09410.4796-0.4120.03450.1619-0.0271-0.00510.0824-0.03420.0356-32.319-30.2222-13.1005
71.59060.5198-0.76542.18651.051.2180.02560.02660.0231-0.1484-0.00580.0204-0.1307-0.003-0.01980.0884-0.006-0.00240.0381-0.00150.0418-22.0391-11.3585-13.0451
81.80791.1853-1.59572.978-0.34911.83920.05710.1620.1212-0.2226-0.00690.2561-0.0555-0.1374-0.05030.0960.0109-0.01780.05220.01610.0428-25.7043-10.14-14.5242
91.7776-1.8769-0.41066.35771.04682.44420.02430.2104-0.1114-0.2809-0.05020.0615-0.0066-0.13990.02590.0599-0.01060.00860.0377-0.01590.009-21.7004-17.3065-19.5901
101.43550.4807-0.91471.8035-0.63130.6478-0.0069-0.0037-0.1849-0.13-0.1303-0.1260.03220.02630.13720.0902-0.01140.00590.0229-0.00720.0579-20.669-16.759-12.1525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 84
2X-RAY DIFFRACTION2A85 - 109
3X-RAY DIFFRACTION3A110 - 118
4X-RAY DIFFRACTION4A119 - 132
5X-RAY DIFFRACTION5A133 - 145
6X-RAY DIFFRACTION6B79 - 83
7X-RAY DIFFRACTION7B84 - 100
8X-RAY DIFFRACTION8B101 - 116
9X-RAY DIFFRACTION9B117 - 132
10X-RAY DIFFRACTION10B133 - 145

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