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- PDB-4pel: S1C mutant of Penicillin G acylase from Kluyvera citrophila -

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Basic information

Entry
Database: PDB / ID: 4pel
TitleS1C mutant of Penicillin G acylase from Kluyvera citrophila
Components
  • Penicillin G acylase subunit alpha
  • Penicillin G acylase subunit beta
KeywordsHYDROLASE / Ntn hydrolase / PGA / slow processing
Function / homology
Function and homology information


penicillin amidase / penicillin amidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Helix Hairpins - #150 / Penicillin G acylase, C-terminal / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase ...Helix Hairpins - #150 / Penicillin G acylase, C-terminal / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Penicillin G acylase / Penicillin G acylase
Similarity search - Component
Biological speciesKluyvera cryocrescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRamasamy, S. / Chand, D. / Varshney, N.K. / Brannigan, J.A. / Wilkinson, A.J. / Suresh, C.G.
CitationJournal: To Be Published
Title: Penicillin G acylase
Authors: Ramasamy, S. / Chand, D. / Wilkinson, A.J. / Brannigan, J.A. / Varshney, N.K. / Suresh, C.G.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin G acylase subunit alpha
B: Penicillin G acylase subunit beta
C: Penicillin G acylase subunit alpha
D: Penicillin G acylase subunit beta
E: Penicillin G acylase subunit alpha
F: Penicillin G acylase subunit beta
G: Penicillin G acylase subunit alpha
H: Penicillin G acylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,60212
Polymers351,4418
Non-polymers1604
Water61334
1
A: Penicillin G acylase subunit alpha
B: Penicillin G acylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9003
Polymers87,8602
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-95 kcal/mol
Surface area28310 Å2
MethodPISA
2
C: Penicillin G acylase subunit alpha
D: Penicillin G acylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9003
Polymers87,8602
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-95 kcal/mol
Surface area28510 Å2
MethodPISA
3
E: Penicillin G acylase subunit alpha
F: Penicillin G acylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9003
Polymers87,8602
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-92 kcal/mol
Surface area28340 Å2
MethodPISA
4
G: Penicillin G acylase subunit alpha
H: Penicillin G acylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9003
Polymers87,8602
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-93 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.260, 96.260, 100.206
Angle α, β, γ (deg.)69.27, 69.27, 76.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALAAA3 - 19629 - 222
21PROPROALAALACC3 - 19629 - 222
12PROPROALAALAAA3 - 19629 - 222
22PROPROALAALAEE3 - 19629 - 222
13PROPROALAALAAA3 - 19629 - 222
23PROPROALAALAGG3 - 19629 - 222
14CYSCYSARGARGBB1 - 5571 - 557
24CYSCYSARGARGDD1 - 5571 - 557
15CYSCYSARGARGBB1 - 5571 - 557
25CYSCYSARGARGFF1 - 5571 - 557
16CYSCYSARGARGBB1 - 5571 - 557
26CYSCYSARGARGHH1 - 5571 - 557
17PROPROALAALACC3 - 19629 - 222
27PROPROALAALAEE3 - 19629 - 222
18PROPROALAALACC3 - 19629 - 222
28PROPROALAALAGG3 - 19629 - 222
19CYSCYSARGARGDD1 - 5571 - 557
29CYSCYSARGARGFF1 - 5571 - 557
110CYSCYSARGARGDD1 - 5571 - 557
210CYSCYSARGARGHH1 - 5571 - 557
111PROPROALAALAEE3 - 19629 - 222
211PROPROALAALAGG3 - 19629 - 222
112CYSCYSARGARGFF1 - 5571 - 557
212CYSCYSARGARGHH1 - 5571 - 557

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Penicillin G acylase subunit alpha / Penicillin G amidase / Penicillin amidohydrolase


Mass: 24887.352 Da / Num. of mol.: 4 / Fragment: UNP residues 1-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyvera cryocrescens (bacteria) / Gene: pac / Production host: Escherichia coli (E. coli) / References: UniProt: P07941, penicillin amidase
#2: Protein
Penicillin G acylase subunit beta / Penicillin G amidase / Penicillin amidohydrolase


Mass: 62972.996 Da / Num. of mol.: 4 / Mutation: S1C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyvera cryocrescens (bacteria) / Gene: pac / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: P07941, UniProt: A0A068F6N5*PLUS, penicillin amidase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Na cacodylate 50mM pH 5.6 Peg 4000 16% (w/v) Na thiocyante 0.5 M NaCl 50 mM Isoproponal 10% (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 68030 / % possible obs: 88.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.9 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3A

1e3a


Resolution: 2.8→38.24 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25142 3420 5 %RANDOM
Rwork0.21385 ---
obs0.21577 64608 88.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-1.54 Å2-1.2 Å2
2---0.48 Å2-0.82 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23696 0 4 34 23734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224364
X-RAY DIFFRACTIONr_bond_other_d00.0222400
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.93133172
X-RAY DIFFRACTIONr_angle_other_deg3.663351508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2752996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39724.5581176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.332153812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0115120
X-RAY DIFFRACTIONr_chiral_restr0.0770.23464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02128196
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025876
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_it2.9244.69712004
X-RAY DIFFRACTIONr_mcbond_other2.9244.69712003
X-RAY DIFFRACTIONr_mcangle_it4.667.0414992
X-RAY DIFFRACTIONr_mcangle_other4.667.04114993
X-RAY DIFFRACTIONr_scbond_it3.234.97412360
X-RAY DIFFRACTIONr_scbond_other3.234.97412361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1997.34218181
X-RAY DIFFRACTIONr_long_range_B_refined8.07638.08328128
X-RAY DIFFRACTIONr_long_range_B_other8.07538.08428129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101130.13
12C101130.13
21A102700.12
22E102700.12
31A103080.13
32G103080.13
41B302810.12
42D302810.12
51B309680.1
52F309680.1
61B304610.12
62H304610.12
71C101370.13
72E101370.13
81C102350.12
82G102350.12
91D306170.11
92F306170.11
101D302530.12
102H302530.12
111E104740.11
112G104740.11
121F308090.11
122H308090.11
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 272 -
Rwork0.327 4636 -
obs--85.91 %

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