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- PDB-2p9b: Crystal structure of putative prolidase from Bifidobacterium longum -

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Basic information

Entry
Database: PDB / ID: 2p9b
TitleCrystal structure of putative prolidase from Bifidobacterium longum
ComponentsPossible prolidase
KeywordsHYDROLASE / Protein Structure Initiative II / PSI-2 / 9350a / Amidohydrolase / Prolidase / Structural Genomics / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Similarity search - Function
Amidohydrolase / Amidohydrolase / Amidohydrolase / Translation Initiation Factor IF3 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase ...Amidohydrolase / Amidohydrolase / Amidohydrolase / Translation Initiation Factor IF3 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Roll / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Possible prolidase (X-Pro dipeptidase) or chlorohydrolase
Similarity search - Component
Biological speciesBifidobacterium longum NCC2705 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative prolidase from Bifidobacterium longum
Authors: Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible prolidase


Theoretical massNumber of molelcules
Total (without water)48,6511
Polymers48,6511
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.649, 63.045, 56.248
Angle α, β, γ (deg.)90.00, 101.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Possible prolidase / Possible X-Pro dipeptidase / possible chlorohydrolase


Mass: 48651.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum NCC2705 (bacteria)
Species: Bifidobacterium longum / Strain: NCC 2705 / Gene: BL1453 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G4D5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12% PEG 6000, 0.1M Citric acid pH 5.0, 0.05 M Magnesium chloride, 5% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 53450 / Num. obs: 53450 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 20
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2701 / Rsym value: 0.225 / % possible all: 57.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→40.27 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 159992.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The missing residues listed in Remark 465 are due to poor or lack of electron density in that region.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2666 5 %RANDOM
Rwork0.193 ---
all0.193 52814 --
obs0.193 52814 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.905 Å2 / ksol: 0.380306 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.58 Å20 Å21.65 Å2
2--2.75 Å20 Å2
3---0.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 0 289 3277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 311 5.1 %
Rwork0.223 5789 -
obs--65.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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