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- PDB-5cde: R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris -

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Basic information

Entry
Database: PDB / ID: 5cde
TitleR372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris
ComponentsProline dipeptidase
KeywordsHYDROLASE / Xaa-Pro dipeptidase / Xanthomonas campestris / prolidase
Function / homology
Function and homology information


: / 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 / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family 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 / 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
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
CitationJournal: To Be Published
Title: R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris at 1.85 Angstrom resolution
Authors: Kumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline dipeptidase
B: Proline dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,00712
Polymers85,2612
Non-polymers74610
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-337 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.088, 101.947, 111.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proline dipeptidase


Mass: 42630.359 Da / Num. of mol.: 2 / Mutation: R372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Strain: ATCC 33913 / NCPPB 528 / LMG 568 / Gene: pepQ, XCC2409 / Plasmid: pST50Tr / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8P839
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: 0.1 M BisTris pH 5.5, 0.2 M Lithium sulphate, 25 % PEG 3350, 1 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1.28225 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2015 / Details: x-ray mirror
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28225 Å / Relative weight: 1
ReflectionResolution: 1.85→46.36 Å / Num. obs: 77891 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Net I/σ(I): 20.1 / Num. measured all: 539390 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.85-1.895.50.6862.11964735890.80.31979.8
9.43-46.365.90.0335440276810.9990.01497.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
PHENIX1.9_1692refinement
RESOLVEphasing
SOLVEphasing
Aimless0.5.7data scaling
XDSdata processing
RefinementMethod to determine structure: SAD / Resolution: 1.85→34.921 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 3877 4.99 %Random selection
Rwork0.1846 73804 --
obs0.1866 77681 97.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.99 Å2 / Biso mean: 32.2078 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 1.85→34.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 22 533 6537
Biso mean--39.61 36.07 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076134
X-RAY DIFFRACTIONf_angle_d1.0978370
X-RAY DIFFRACTIONf_chiral_restr0.042934
X-RAY DIFFRACTIONf_plane_restr0.0051116
X-RAY DIFFRACTIONf_dihedral_angle_d13.0512184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.87260.29491150.25952065218078
1.8726-1.89630.3361090.26292240234984
1.8963-1.92120.27171220.2492380250289
1.9212-1.94750.27581380.23692576271497
1.9475-1.97540.29321220.228326802802100
1.9754-2.00480.28951420.215726452787100
2.0048-2.03620.26151330.208326832816100
2.0362-2.06950.27671530.212526772830100
2.0695-2.10520.24141450.218326382783100
2.1052-2.14350.261270.210626822809100
2.1435-2.18470.29411400.205726582798100
2.1847-2.22930.26611560.200726602816100
2.2293-2.27780.23041540.192526512805100
2.2778-2.33080.21461330.192226632796100
2.3308-2.3890.26221370.19032669280699
2.389-2.45360.26071570.197926542811100
2.4536-2.52580.26991340.20242685281999
2.5258-2.60730.29691280.19592693282199
2.6073-2.70040.22521320.19852675280799
2.7004-2.80850.27291440.20952674281899
2.8085-2.93630.25151500.20272666281699
2.9363-3.0910.22811340.19812697283199
3.091-3.28450.24261580.188226932851100
3.2845-3.53790.20091270.17762720284799
3.5379-3.89350.15241680.151926882856100
3.8935-4.45590.17021450.143227492894100
4.4559-5.61020.17441300.149527802910100
5.6102-34.92720.21311440.17232863300798
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)
10.89190.46220.69622.27432.30164.0717-0.03490.11450.4932-0.5383-0.1590.0298-1.2685-0.24150.05620.7323-0.0618-0.03710.30.09620.469939.513268.53651.5146
23.33520.5250.03160.75170.05880.86460.00360.4675-0.0025-0.16750.0335-0.02790.07980.1076-0.03310.25790.03540.00030.27080.00450.190931.166833.466541.058
30.75050.00540.00041.24930.12791.943-0.0242-0.01660.13390.0383-0.0351-0.0843-0.30060.2230.05780.1951-0.06110.00160.22940.01790.239344.405254.357663.9035
40.4260.083-0.03862.4015-2.26953.1453-0.2814-0.0380.51140.1561-0.0358-0.08-0.76160.13160.34520.5578-0.0019-0.18010.2642-0.00110.48399.101365.153660.7615
54.44290.53510.32830.5753-0.01280.88830.0074-0.5442-0.08120.1157-0.0003-0.0359-0.0172-0.0701-0.00380.21860.0085-0.00210.24390.01240.18324.18835.070171.5295
64.77331.36540.22422.6318-2.13986.5167-0.0137-0.4709-0.34090.1607-0.0365-0.15510.1565-0.03650.0680.23790.0633-0.01830.1951-0.00670.283328.176124.892367.7395
76.564-3.001-1.09162.59790.44340.5617-0.01330.0366-0.2334-0.02750.00380.08710.07430.02830.02960.21410.0123-0.01980.20140.00840.179820.71828.307961.8866
81.99691.1321-1.04634.1935-2.92274.1956-0.35430.05790.4586-0.1346-0.0144-0.0869-0.62460.24910.27040.3904-0.0829-0.16830.21050.03120.444511.781761.18954.4028
90.0454-0.20590.00651.0403-0.1632.0341-0.23220.40630.265-0.29410.0377-0.2838-0.1170.45680.18070.4228-0.2221-0.09060.48110.15710.450116.141157.763841.9753
100.87670.05030.61340.86050.26111.8055-0.14980.12090.1767-0.16950.07240.1473-0.113-0.00020.06750.1852-0.0337-0.05510.16780.05110.25253.295246.657346.2131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )A
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 169 )A
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 399 )A
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 29 )B
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 115 )B
6X-RAY DIFFRACTION6chain 'B' and (resid 116 through 139 )B
7X-RAY DIFFRACTION7chain 'B' and (resid 140 through 169 )B
8X-RAY DIFFRACTION8chain 'B' and (resid 170 through 214 )B
9X-RAY DIFFRACTION9chain 'B' and (resid 215 through 246 )B
10X-RAY DIFFRACTION10chain 'B' and (resid 247 through 399 )B

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