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- PDB-5cnx: Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12 -

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Basic information

Entry
Database: PDB / ID: 5cnx
TitleCrystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12
ComponentsAminopeptidase YpdF
KeywordsHYDROLASE / Xaa-Pro aminopeptidase / PepQ / prolidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloaminopeptidase activity / transition metal ion binding / aminopeptidase activity / protein homodimerization activity / proteolysis
Similarity search - Function
: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 ...: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Aminopeptidase YpdF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.D.
CitationJournal: Proteins / Year: 2018
Title: Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases
Authors: Are, V.N. / Kumar, A. / Goyal, V.D. / Gotad, S.S. / Ghosh, B. / Gadre, R. / Jamdar, S.N. / Makde, R.D.
History
DepositionJul 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 16, 2019Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase YpdF
B: Aminopeptidase YpdF
C: Aminopeptidase YpdF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,78014
Polymers118,8623
Non-polymers91911
Water90150
1
A: Aminopeptidase YpdF
C: Aminopeptidase YpdF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,89210
Polymers79,2412
Non-polymers6518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase YpdF
hetero molecules

B: Aminopeptidase YpdF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7778
Polymers79,2412
Non-polymers5366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_979-x+4,-x+y+2,-z+14/31
Unit cell
Length a, b, c (Å)224.202, 224.202, 74.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Aminopeptidase YpdF


Mass: 39620.641 Da / Num. of mol.: 3 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Details: genomic DNA / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ypdF, b2385, JW2382 / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P76524, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 61 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 4.56 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: microbatch
Details: Crystallization solution: 1.4 M Sodium Citrate, 0.1 M Sodium Cacodylate pH 6.6, 10% glycerol, 1 mM ZnCl2 Protein solution: 20 mM TrisHCl, 200 mM NaCl
PH range: 7.2-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 6, 2014 / Details: mirror
RadiationMonochromator: doule crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.6→48.9 Å / Num. obs: 66134 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata processing
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6D

3q6d


Resolution: 2.6→48.897 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 3344 5.06 %Random selection
Rwork0.2188 ---
obs0.2199 66107 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8293 0 28 50 8371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078475
X-RAY DIFFRACTIONf_angle_d0.99511522
X-RAY DIFFRACTIONf_dihedral_angle_d13.6443056
X-RAY DIFFRACTIONf_chiral_restr0.0391324
X-RAY DIFFRACTIONf_plane_restr0.0051502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63720.35561410.31962604X-RAY DIFFRACTION100
2.6372-2.67650.3281430.31472591X-RAY DIFFRACTION100
2.6765-2.71840.33831400.3042594X-RAY DIFFRACTION100
2.7184-2.76290.3281340.29932601X-RAY DIFFRACTION100
2.7629-2.81060.33131200.29482598X-RAY DIFFRACTION100
2.8106-2.86170.30131390.28412621X-RAY DIFFRACTION100
2.8617-2.91670.31111440.27972584X-RAY DIFFRACTION100
2.9167-2.97620.29531410.28842602X-RAY DIFFRACTION100
2.9762-3.04090.34121360.28972586X-RAY DIFFRACTION100
3.0409-3.11160.30861300.28232662X-RAY DIFFRACTION100
3.1116-3.18940.28761390.26512571X-RAY DIFFRACTION100
3.1894-3.27570.2971510.25342607X-RAY DIFFRACTION100
3.2757-3.3720.27371540.23052585X-RAY DIFFRACTION100
3.372-3.48080.2041340.23012601X-RAY DIFFRACTION100
3.4808-3.60520.24951350.21932616X-RAY DIFFRACTION100
3.6052-3.74950.23811470.22052614X-RAY DIFFRACTION100
3.7495-3.92010.22291270.20272635X-RAY DIFFRACTION100
3.9201-4.12670.19991450.19062599X-RAY DIFFRACTION100
4.1267-4.38510.17971450.17172625X-RAY DIFFRACTION100
4.3851-4.72340.20071250.15642650X-RAY DIFFRACTION100
4.7234-5.19820.18071360.16982628X-RAY DIFFRACTION100
5.1982-5.94930.20671530.19462616X-RAY DIFFRACTION100
5.9493-7.49120.22271540.19622664X-RAY DIFFRACTION100
7.4912-48.90590.18641310.17312709X-RAY DIFFRACTION99
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)
10.7454-0.1116-0.14081.00360.82562.8031-0.1860.11910.02440.1864-0.01040.1470.6215-0.11960.15660.3155-0.10870.07470.32280.01090.2466371.30769.7812149.5089
21.27820.4647-0.70352.1983-1.04891.7786-0.0558-0.09-0.2043-0.4246-0.04370.10440.37070.25750.05050.4177-0.01510.00890.30210.00710.2466414.957668.9802162.3319
31.7581-0.1557-0.59420.63660.05271.0831-0.12811.46540.0749-0.13810.0868-0.0178-0.12250.0150.08350.1309-0.2032-0.07091.07130.06790.402357.287882.5913132.9342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:360)
2X-RAY DIFFRACTION2(chain B and resseq 1:360)
3X-RAY DIFFRACTION3(chain C and resseq 1:360)

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