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- PDB-5tro: 1.8 Angstrom Resolution Crystal Structure of Dimerization and Tra... -

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Basic information

Entry
Database: PDB / ID: 5tro
Title1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dimerization Domain / Transpeptidase Domain / Penicillin-Binding Protein 1
Function / homology
Function and homology information


penicillin binding / cell wall organization / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1
B: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6924
Polymers129,6212
Non-polymers712
Water11,079615
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.843, 72.202, 86.362
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1129-

HOH

21B-1037-

HOH

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Components

#1: Protein Penicillin-binding protein 1


Mass: 64810.695 Da / Num. of mol.: 2 / Fragment: UNP residues 39-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp1, SACOL1194 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: A0A0H2WVW5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 98204 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 26.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.793 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.435 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20946 4950 5 %RANDOM
Rwork0.17935 ---
obs0.18088 93238 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-1.07 Å2
2---1.38 Å20 Å2
3---1.39 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7959 0 2 615 8576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198235
X-RAY DIFFRACTIONr_bond_other_d0.0010.027900
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.97211082
X-RAY DIFFRACTIONr_angle_other_deg0.819318300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1395.0191033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82825.147375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.411151439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6961535
X-RAY DIFFRACTIONr_chiral_restr0.0850.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0219393
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021850
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_it1.0662.1834097
X-RAY DIFFRACTIONr_mcbond_other1.0652.1824096
X-RAY DIFFRACTIONr_mcangle_it1.7393.2645134
X-RAY DIFFRACTIONr_mcangle_other1.7393.2655135
X-RAY DIFFRACTIONr_scbond_it1.1832.3544138
X-RAY DIFFRACTIONr_scbond_other1.1832.3554139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9413.455948
X-RAY DIFFRACTIONr_long_range_B_refined5.18626.6069378
X-RAY DIFFRACTIONr_long_range_B_other5.02826.1349255
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 344 -
Rwork0.305 6462 -
obs--93.32 %
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)
11.1981.10361.07451.66761.54623.02620.1096-0.199-0.15990.32840.0121-0.15050.25570.219-0.12180.1567-0.0276-0.09240.22810.05170.258822.5054-19.786419.7495
27.5616-1.9813-2.71967.96293.956511.7119-0.14140.0953-0.26950.60520.314-0.53160.00870.7035-0.17260.1138-0.0928-0.12450.36890.02180.228942.9178-8.984236.7008
37.6051.47021.08185.83022.48752.8671-0.02070.5065-0.6327-0.15580.2808-0.6905-0.14380.5441-0.26010.0959-0.0827-0.05620.3615-0.03460.176138.3684-11.122328.6511
40.73830.0081-0.13810.67480.21321.48780.04550.0816-0.0564-0.0678-0.0331-0.0953-0.10640.0878-0.01240.0267-0.0091-0.03990.05040.02190.196322.0343-22.7282-7.0164
50.99230.2747-0.16190.87980.41451.9870.03370.3299-0.0019-0.28010.00610.0053-0.1841-0.051-0.03980.11980.0359-0.04630.15720.00720.140816.2091-22.6076-26.8744
60.89330.0414-0.29210.31240.15382.12510.04730.0951-0.1941-0.0587-0.0125-0.0090.1479-0.0865-0.03480.0516-0.0011-0.07390.0458-0.02810.23213.0107-34.2109-12.4896
71.71740.3194-0.07291.4251-0.17051.72540.04970.2496-0.2167-0.151-0.0093-0.12040.10870.2564-0.04040.03220.0192-0.02630.1025-0.03190.191328.7003-29.9356-15.4398
83.4636-1.3985-1.41520.71630.61150.98290.14930.30430.2363-0.17720.0186-0.0636-0.2070.0665-0.1680.1868-0.10840.03170.23480.01280.305533.32611.0439-12.7735
94.19790.5057-0.07996.21860.5751.9785-0.0342-0.0965-0.10380.08070.0608-0.28970.11970.0088-0.02660.0092-0.01070.00320.1201-0.06680.151652.1452-8.9517-10.6073
107.0674-1.80150.48212.79770.33611.9619-0.20980.06160.55020.08240.0564-0.2196-0.0526-0.18710.15340.0339-0.03210.02030.0833-0.050.159844.17350.0806-12.0507
111.3681-0.0491-0.36850.8580.27641.45690.0648-0.20080.26130.1798-0.0894-0.1187-0.05280.12550.02460.1655-0.0814-0.05230.0661-0.0190.282517.58216.894114.0613
121.4637-0.1587-0.65450.8942-0.03632.63870.0654-0.38260.27830.3301-0.10720.0008-0.14060.07690.04180.227-0.1093-0.00130.1506-0.10670.27735.30248.432924.5963
131.9073-0.5722-1.05490.84920.48732.27870.2209-0.49310.65130.2612-0.0585-0.0598-0.4308-0.0374-0.16240.4719-0.1474-0.01540.2439-0.21980.55448.983419.945326.415
142.4726-0.2977-0.19751.3404-0.52051.99780.0774-0.6150.56590.3128-0.0837-0.1067-0.24580.14490.00620.3026-0.1373-0.07210.2041-0.13660.381920.846915.01924.7513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 90
2X-RAY DIFFRACTION2A91 - 119
3X-RAY DIFFRACTION3A120 - 166
4X-RAY DIFFRACTION4A167 - 352
5X-RAY DIFFRACTION5A353 - 438
6X-RAY DIFFRACTION6A439 - 511
7X-RAY DIFFRACTION7A512 - 590
8X-RAY DIFFRACTION8B61 - 98
9X-RAY DIFFRACTION9B99 - 135
10X-RAY DIFFRACTION10B136 - 166
11X-RAY DIFFRACTION11B167 - 348
12X-RAY DIFFRACTION12B349 - 466
13X-RAY DIFFRACTION13B467 - 521
14X-RAY DIFFRACTION14B522 - 589

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