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- PDB-5cik: Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campest... -

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Basic information

Entry
Database: PDB / ID: 5cik
TitleCrystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition
ComponentsProline dipeptidase
KeywordsHYDROLASE / Xaa-pro dipeptidase / prolidase / M24 family / citrate
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
CITRIC ACID / Proline dipeptidase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKumar, A. / Are, V. / Ghosh, B. / Agrawal, U. / Jamdar, S. / Makde, R.D.
CitationJournal: To Be Published
Title: Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition
Authors: Kumar, A. / Are, V. / Ghosh, B. / Agrawal, U. / Jamdar, S. / Makde, R.D.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 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 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,1766
Polymers85,6072
Non-polymers5684
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-13 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.179, 103.673, 136.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 399 / Label seq-ID: 3 - 399

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Proline dipeptidase


Mass: 42803.555 Da / Num. of mol.: 2 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
Strain: ATCC 33913 / Gene: pepQ, XCC2409 / Plasmid: pST50Tr / Details (production host): pET3a based vector / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8P839, Xaa-Pro dipeptidase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5 / Details: 0.1 M Citric acid, 20% PEG6000 / PH range: 5.0-5.5

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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: Jul 5, 2013 / Details: x-ray mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.2→48.44 Å / Num. obs: 42175 / % possible obs: 98.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 43.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 20.8 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
XDSdata processing
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FKC

4fkc


Resolution: 2.2→44.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.709 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18134 2086 5 %RANDOM
Rwork0.14788 ---
obs0.14957 40022 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.464 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.2→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5984 0 38 518 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196232
X-RAY DIFFRACTIONr_bond_other_d0.0060.025897
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9568511
X-RAY DIFFRACTIONr_angle_other_deg1.118313503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85223.31284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9615929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1761554
X-RAY DIFFRACTIONr_chiral_restr0.0980.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217279
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021467
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_it1.1751.1583197
X-RAY DIFFRACTIONr_mcbond_other1.1751.1583196
X-RAY DIFFRACTIONr_mcangle_it1.8921.7313999
X-RAY DIFFRACTIONr_mcangle_other1.8921.7314000
X-RAY DIFFRACTIONr_scbond_it2.0011.4313035
X-RAY DIFFRACTIONr_scbond_other21.4313035
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1862.0594504
X-RAY DIFFRACTIONr_long_range_B_refined5.18310.0237249
X-RAY DIFFRACTIONr_long_range_B_other4.9419.7537043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24108 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 125 -
Rwork0.129 2667 -
obs--89.92 %

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