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- PDB-5u47: 1.95 Angstrom Resolution Crystal Structure of Penicillin Binding ... -

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Basic information

Entry
Database: PDB / ID: 5u47
Title1.95 Angstrom Resolution Crystal Structure of Penicillin Binding Protein 2X from Streptococcus thermophilus
ComponentsPenicillin binding protein 2X
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Lipid-Binding Protein / hydrolase
Function / homology
Function and homology information


penicillin binding / plasma membrane
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #70 / Alpha-Beta Plaits - #2110 / : / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ubiquitin Ligase Nedd4; Chain: W; ...Ubiquitin Ligase Nedd4; Chain: W; - #70 / Alpha-Beta Plaits - #2110 / : / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Single Sheet / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Penicillin binding protein 2X
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionDec 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords
Revision 1.2Feb 11, 2026Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9304
Polymers76,7761
Non-polymers1543
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-10 kcal/mol
Surface area29620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.535, 78.494, 164.856
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 Penicillin binding protein 2X


Mass: 76776.055 Da / Num. of mol.: 1 / Fragment: residues 52-755 / Mutation: A551T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Strain: ATCC BAA-250 / LMG 18311 / Gene: pbp2X, stu1701 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5M2U8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 8.0 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: Classics II (G6), 0.2M Ammonium acetate, 0.1M Bis-Tris (pH 5.5), 25% (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: Nov 30, 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: 1.95→30 Å / Num. obs: 51840 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 21.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.805 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QME

1qme


Resolution: 1.95→29.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.638 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20966 2547 4.9 %RANDOM
Rwork0.16945 ---
obs0.17146 48993 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.213 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20 Å2
2--1.49 Å20 Å2
3---0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 9 498 5729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025422
X-RAY DIFFRACTIONr_bond_other_d0.0010.025026
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.967344
X-RAY DIFFRACTIONr_angle_other_deg0.847311751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2475707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97826.036222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.76815984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2291516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.026090
X-RAY DIFFRACTIONr_gen_planes_other0.020.021006
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_it1.5432.5042797
X-RAY DIFFRACTIONr_mcbond_other1.5282.52794
X-RAY DIFFRACTIONr_mcangle_it2.5133.743513
X-RAY DIFFRACTIONr_mcangle_other2.5153.7423514
X-RAY DIFFRACTIONr_scbond_it1.7942.7052625
X-RAY DIFFRACTIONr_scbond_other1.7932.7062626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.893.9543832
X-RAY DIFFRACTIONr_long_range_B_refined5.49930.7426299
X-RAY DIFFRACTIONr_long_range_B_other5.3830.2556191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 183 -
Rwork0.264 3554 -
obs--100 %
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)
11.2113-0.6206-0.15760.65880.16940.2007-0.0799-0.056-0.020.20840.1599-0.11820.21810.1494-0.080.26940.1673-0.10450.1498-0.11750.157659.9161-18.778125.8047
21.152-0.7622-0.15750.81240.52881.0391-0.0866-0.0738-0.14060.19220.10020.04150.22940.1045-0.01360.08620.023-0.00630.0214-0.01070.063336.8537-3.751423.645
33.0495-1.0641-0.05541.43710.28391.1174-0.0388-0.32980.20270.2107-0.09120.246-0.1643-0.47870.12990.08830.07130.03690.3007-0.12880.12194.435120.048328.0354
41.087-0.087-0.02630.40880.20271.78190.01270.00170.0986-0.0124-0.10510.0697-0.172-0.43650.09240.02060.0376-0.00490.1294-0.05110.050913.959914.406617.9266
52.29840.2471-0.50721.6368-0.51753.5806-0.0244-0.28850.10250.1528-0.09310.0634-0.2122-0.21550.11750.08280.02810.0070.078-0.04640.06421.101417.96428.6016
61.409-0.26950.76560.7738-0.29611.04750.02330.0248-0.1969-0.10760.08140.07390.1585-0.1023-0.10470.0646-0.0185-0.01590.0639-0.04240.077817.9623-3.45031.4994
76.17261.9046-0.50723.7748-0.68092.5883-0.13310.08070.1441-0.34190.05370.2107-0.1627-0.17150.07940.05510.02-0.03630.0555-0.02370.03034.40617.4972-5.6175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 190
2X-RAY DIFFRACTION2A191 - 332
3X-RAY DIFFRACTION3A333 - 393
4X-RAY DIFFRACTION4A394 - 546
5X-RAY DIFFRACTION5A547 - 624
6X-RAY DIFFRACTION6A625 - 720
7X-RAY DIFFRACTION7A721 - 755

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