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- PDB-4rwr: 2.1 Angstrom Crystal Structure of Stage II Sporulation Protein D ... -

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Basic information

Entry
Database: PDB / ID: 4rwr
Title2.1 Angstrom Crystal Structure of Stage II Sporulation Protein D from Bacillus anthracis
ComponentsStage II sporulation protein D
KeywordsVIRAL PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / stage II sporulation protein D / SpoIID / germination
Function / homologySporulation stage II protein D, amidase enhancer LytB / Sporulation stage II protein D, amidase enhancer LytB N-terminal / Sporulation stage II, protein D firmicutes / Stage II sporulation protein / : / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / Stage II sporulation protein D / Stage II sporulation protein D
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMinasov, G. / Wawrzak, Z. / Nocadello, S. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. ...Minasov, G. / Wawrzak, Z. / Nocadello, S. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation.
Authors: Nocadello, S. / Minasov, G. / Shuvalova, L.S. / Dubrovska, I. / Sabini, E. / Anderson, W.F.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stage II sporulation protein D
B: Stage II sporulation protein D


Theoretical massNumber of molelcules
Total (without water)74,1112
Polymers74,1112
Non-polymers00
Water5,224290
1
A: Stage II sporulation protein D


Theoretical massNumber of molelcules
Total (without water)37,0551
Polymers37,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Stage II sporulation protein D


Theoretical massNumber of molelcules
Total (without water)37,0551
Polymers37,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.616, 144.477, 47.076
Angle α, β, γ (deg.)90.00, 115.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Stage II sporulation protein D / Stage II sporulation protein D (SpoIID)


Mass: 37055.449 Da / Num. of mol.: 2 / Fragment: UNP residues 32-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: BAS5136, BA_5528, DH23_5378, DJ42_3419, DJ44_3608, DJ45_519, DJ48_4453, DJ49_4581, GBAA_5528, spoIID
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q81K14, UniProt: A0A6L7HNW1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 6.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer, pH 8.3, 2mM N-Acetylglucosamine; Screen: Classics II (H7), 0.15M DL-Malic acid, pH 7.0, 20% (w/v) PEG 3350, VAPOR ...Details: Protein: 6.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer, pH 8.3, 2mM N-Acetylglucosamine; Screen: Classics II (H7), 0.15M DL-Malic acid, pH 7.0, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2014 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 32915 / Num. obs: 32915 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1648 / Rsym value: 0.623 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→27.53 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.827 / SU ML: 0.149
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24348 1657 5.1 %RANDOM
Rwork0.18752 ---
obs0.19033 31083 99.93 %-
all-31083 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.359 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20.1 Å2
2---2.37 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 0 290 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024427
X-RAY DIFFRACTIONr_bond_other_d0.0010.024191
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9555977
X-RAY DIFFRACTIONr_angle_other_deg0.73339694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8935565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.21325.288208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.8515782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.661520
X-RAY DIFFRACTIONr_chiral_restr0.0970.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021005
X-RAY DIFFRACTIONr_mcbond_it2.0072.4912221
X-RAY DIFFRACTIONr_mcbond_other2.0042.4892220
X-RAY DIFFRACTIONr_mcangle_it3.0593.7132799
X-RAY DIFFRACTIONr_mcangle_other3.0593.7162800
X-RAY DIFFRACTIONr_scbond_it2.6832.8572206
X-RAY DIFFRACTIONr_scbond_other2.6822.8592207
X-RAY DIFFRACTIONr_scangle_other4.1854.1433179
X-RAY DIFFRACTIONr_long_range_B_refined6.86921.1945357
X-RAY DIFFRACTIONr_long_range_B_other6.76120.9375266
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 118 -
Rwork0.246 2284 -
obs-2284 99.92 %
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)
10.45032.3797-0.409113.2797-1.60691.3163-0.029-0.01110.0261-0.34680.08640.3012-0.06160.0129-0.05740.0973-0.0085-0.02640.06970.08290.1096-4.110829.15335.3595
22.79810.1211.46071.7613-0.24381.52360.03260.32150.1773-0.16510.11630.1667-0.0099-0.0923-0.14880.0763-0.00810.02760.13530.09690.1075-3.979817.083510.5716
30.9282-0.0348-0.22351.55230.47651.37580.02090.00970.0450.12170.0678-0.06030.02590.138-0.08870.0743-0.0184-0.04870.06160.00220.040712.91850.528620.6002
43.3779-1.576-1.20971.77740.12951.9568-0.0334-0.02760.13060.07160.1038-0.10430.18060.1817-0.07040.1371-0.016-0.07180.1081-0.01560.071612.3109-0.976517.9452
52.7031-0.80750.58538.2196-1.11584.15230.0114-0.20940.40570.4870.30510.0676-0.3914-0.4923-0.31640.10250.04570.08250.11720.01520.1333-6.997119.191524.3321
61.3999-3.7848-0.162215.55770.80360.08930.0442-0.0665-0.04930.4106-0.0219-0.2211-0.0138-0.0551-0.02230.0980.0251-0.03470.06940.0370.06899.2551-45.005120.7348
70.3927-0.88720.03443.39041.54692.4389-0.1218-0.10780.00810.27220.1361-0.13890.10640.1367-0.01430.14320.0690.03090.18970.02940.16454.3077-35.683714.2185
81.3272-0.28460.19872.3466-0.44861.7814-0.1431-0.2024-0.12980.24420.07410.01790.1120.12770.06890.05330.03920.02440.05680.01610.03641.7994-30.74615.0084
91.22370.3167-0.23662.0999-0.03932.0801-0.04530.10210.0049-0.01490.0264-0.11980.00380.16640.01890.0389-0.0063-0.0270.0879-0.00680.02888.5843-12.1493-3.9317
102.21570.2544-0.63812.7221-0.58981.7005-0.1594-0.3114-0.26760.17190.030.27030.13030.00390.12940.04990.0190.04290.08610.02830.0817-5.6573-30.831814.2119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 87
2X-RAY DIFFRACTION2A88 - 179
3X-RAY DIFFRACTION3A180 - 246
4X-RAY DIFFRACTION4A247 - 308
5X-RAY DIFFRACTION5A309 - 331
6X-RAY DIFFRACTION6B63 - 88
7X-RAY DIFFRACTION7B89 - 131
8X-RAY DIFFRACTION8B132 - 205
9X-RAY DIFFRACTION9B206 - 288
10X-RAY DIFFRACTION10B289 - 333

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