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- PDB-4ye5: The crystal structure of a peptidoglycan synthetase from Bifidoba... -

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Basic information

Entry
Database: PDB / ID: 4ye5
TitleThe crystal structure of a peptidoglycan synthetase from Bifidobacterium adolescentis ATCC 15703
ComponentsPeptidoglycan synthetase penicillin-binding protein 3
Keywordspenicillin binding protein / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


penicillin binding / integral component of membrane
Similarity search - Function
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/transpeptidase-like
Similarity search - Domain/homology
ACETATE ION / Peptidoglycan synthetase penicillin-binding protein 3
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.052 Å
AuthorsCuff, M. / Tan, K. / Joachimiak, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: The crystal structure of a peptidoglycan synthetase from Bifidobacterium adolescentis ATCC 15703
Authors: Cuff, M. / Tan, K. / Joachimiak, G. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan synthetase penicillin-binding protein 3
B: Peptidoglycan synthetase penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5278
Polymers122,0072
Non-polymers5206
Water9,998555
1
A: Peptidoglycan synthetase penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4646
Polymers61,0041
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan synthetase penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0632
Polymers61,0041
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.956, 85.709, 227.476
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 Peptidoglycan synthetase penicillin-binding protein 3


Mass: 61003.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a) (bacteria)
Strain: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a / Gene: ftsI, BAD_1107 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: A1A2F5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Bis-Tris Propane:NaOH, 1.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 102844 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 36.37
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.58 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.052→47.387 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 5101 4.96 %Random selection
Rwork0.189 ---
obs0.1908 102844 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.052→47.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 34 555 8533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088128
X-RAY DIFFRACTIONf_angle_d1.03311027
X-RAY DIFFRACTIONf_dihedral_angle_d13.7292927
X-RAY DIFFRACTIONf_chiral_restr0.0711283
X-RAY DIFFRACTIONf_plane_restr0.0041448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0522-2.07550.317960.23461934X-RAY DIFFRACTION59
2.0755-2.09990.25871210.23982505X-RAY DIFFRACTION75
2.0999-2.12560.28091640.22963030X-RAY DIFFRACTION92
2.1256-2.15250.27211640.22483193X-RAY DIFFRACTION96
2.1525-2.18080.28321680.21933242X-RAY DIFFRACTION99
2.1808-2.21070.24711840.20933346X-RAY DIFFRACTION100
2.2107-2.24220.25941910.20253261X-RAY DIFFRACTION100
2.2422-2.27570.23581580.19583320X-RAY DIFFRACTION100
2.2757-2.31130.21551690.19473332X-RAY DIFFRACTION100
2.3113-2.34920.26821680.19253285X-RAY DIFFRACTION100
2.3492-2.38970.20791540.1853387X-RAY DIFFRACTION100
2.3897-2.43310.20341790.18563312X-RAY DIFFRACTION100
2.4331-2.47990.22331600.18433350X-RAY DIFFRACTION100
2.4799-2.53050.24271750.18133337X-RAY DIFFRACTION100
2.5305-2.58560.2361870.19293329X-RAY DIFFRACTION100
2.5856-2.64570.22841800.19353272X-RAY DIFFRACTION100
2.6457-2.71190.25621580.19593359X-RAY DIFFRACTION100
2.7119-2.78520.23531800.19573336X-RAY DIFFRACTION100
2.7852-2.86710.24961970.18983331X-RAY DIFFRACTION100
2.8671-2.95960.22671850.19443351X-RAY DIFFRACTION100
2.9596-3.06540.23652090.19133290X-RAY DIFFRACTION100
3.0654-3.18810.2271900.19413341X-RAY DIFFRACTION100
3.1881-3.33320.2251610.19373359X-RAY DIFFRACTION100
3.3332-3.50890.19971640.19263363X-RAY DIFFRACTION100
3.5089-3.72860.22031750.18293407X-RAY DIFFRACTION100
3.7286-4.01640.19161810.16683363X-RAY DIFFRACTION100
4.0164-4.42030.1841760.16233394X-RAY DIFFRACTION100
4.4203-5.05930.19451470.16143502X-RAY DIFFRACTION100
5.0593-6.37170.20851860.19053416X-RAY DIFFRACTION100
6.3717-47.39940.2391740.20173496X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0347-0.32390.07982.62490.5585-0.1659-0.04220.014-0.06860.12570.0043-0.02620.1180.04470.03120.34140.02490.06460.1466-0.03250.27763.445172.469596.5376
21.4857-0.1965-0.44351.68850.10911.58140.0129-0.20350.16090.2329-0.03970.1593-0.1033-0.01750.0340.16110.01210.00110.1064-0.04150.1862-6.5232110.7357111.4814
31.1274-0.4957-0.43690.27320.18250.12340.16120.83730.1348-0.2173-0.02910.3641-0.00230.5543-0.09210.14580.34170.25121.53760.01060.5702-44.7777114.398877.7437
41.02830.61980.53141.75440.00752.82770.04891.161-0.2186-0.31540.023-0.37740.15740.0866-0.00170.33710.09880.06990.883-0.20710.21971.3258100.644363.2473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 333 )
2X-RAY DIFFRACTION2chain 'A' and (resid 334 through 600 )
3X-RAY DIFFRACTION3chain 'B' and (resid 55 through 254 )
4X-RAY DIFFRACTION4chain 'B' and (resid 255 through 600 )

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