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- PDB-7rep: Crystal structure of an engineered variant of single-chain Penici... -

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Basic information

Entry
Database: PDB / ID: 7rep
TitleCrystal structure of an engineered variant of single-chain Penicillin G Acylase from Kluyvera cryocrescens (A1-Ac Rd3CHis)
ComponentsPenicillin G acylase
KeywordsHYDROLASE / penicillin / acylase
Function / homologyphenylmethanesulfonic acid
Function and homology information
Biological speciesKluyvera cryocrescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.192 Å
AuthorsOrth, P.
CitationJournal: Science / Year: 2022
Title: A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins.
Authors: Fryszkowska, A. / An, C. / Alvizo, O. / Banerjee, G. / Canada, K.A. / Cao, Y. / DeMong, D. / Devine, P.N. / Duan, D. / Elgart, D.M. / Farasat, I. / Gauthier, D.R. / Guidry, E.N. / Jia, X. / ...Authors: Fryszkowska, A. / An, C. / Alvizo, O. / Banerjee, G. / Canada, K.A. / Cao, Y. / DeMong, D. / Devine, P.N. / Duan, D. / Elgart, D.M. / Farasat, I. / Gauthier, D.R. / Guidry, E.N. / Jia, X. / Kong, J. / Kruse, N. / Lexa, K.W. / Makarov, A.A. / Mann, B.F. / Milczek, E.M. / Mitchell, V. / Nazor, J. / Neri, C. / Orr, R.K. / Orth, P. / Phillips, E.M. / Riggins, J.N. / Schafer, W.A. / Silverman, S.M. / Strulson, C.A. / Subramanian, N. / Voladri, R. / Yang, H. / Yang, J. / Yi, X. / Zhang, X. / Zhong, W.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin G acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4713
Polymers86,2591
Non-polymers2122
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.700, 102.700, 255.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Penicillin G acylase


Mass: 86259.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyvera cryocrescens (bacteria) / Production host: Escherichia coli (E. coli) / References: penicillin amidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2M Ammonium sulfate, 100mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.192→50 Å / Num. obs: 70875 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 19
Reflection shellResolution: 2.192→2.28 Å / Num. unique obs: 6972 / CC1/2: 0.399

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (11-DEC-2020)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PEM

4pem


Resolution: 2.192→47.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1396 1.97 %RANDOM
Rwork0.2248 ---
obs0.2254 70766 99.8 %-
Displacement parametersBiso max: 92.09 Å2 / Biso mean: 46.01 Å2 / Biso min: 26.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.4151 Å20 Å20 Å2
2---0.4151 Å20 Å2
3---0.8302 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.192→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 11 236 6269
Biso mean--53.77 44.88 -
Num. residues----764
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2053SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1065HARMONIC5
X-RAY DIFFRACTIONt_it6211HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion781SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5333SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6211HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8467HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion17.57
LS refinement shellResolution: 2.192→2.21 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4289 25 1.77 %
Rwork0.358 1391 -
obs--92.53 %

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