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- PDB-2iw2: Crystal structure of human Prolidase -

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Basic information

Entry
Database: PDB / ID: 2iw2
TitleCrystal structure of human Prolidase
ComponentsXAA-PRO DIPEPTIDASE
KeywordsHYDROLASE / METALLOCARBOXYPEPTIDASE / DISEASE MUTATION / XAA-PRO DIPEPTIDASE / DIPEPTIDASE / PEPTIDASE D / COLLAGEN DEGRADATION / METALLOAMINOPEPTIDASE / ENZYME / PROTEASE / PEPD GENE / MANGANESE / METAL- BINDING / METALLOPROTEASE / PHOSPHORYLATION
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / negative regulation of programmed cell death / amino acid metabolic process / metalloaminopeptidase activity / collagen catabolic process / metallocarboxypeptidase activity / manganese ion binding / peptidase activity / proteolysis / extracellular exosome
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
AuthorsMueller, U. / Niesen, F.H. / Roske, Y. / Goetz, F. / Behlke, J. / Buessow, K. / Heinemann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Prolidase: The Molecular Basis of Pd Disease
Authors: Mueller, U. / Niesen, F.H. / Roske, Y. / Goetz, F. / Behlke, J. / Buessow, K. / Heinemann, U.
History
DepositionJun 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XAA-PRO DIPEPTIDASE
B: XAA-PRO DIPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4397
Polymers109,3242
Non-polymers1155
Water17,853991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.579, 108.518, 211.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.07789, 0.04202, -0.9961), (0.03623, -0.9983, -0.04495), (-0.9963, -0.03959, 0.07624)
Vector: 164.9, 59, 155)

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Components

#1: Protein XAA-PRO DIPEPTIDASE / PROLIDASE / X-PRO DIPEPTIDASE / PROLINE DIPEPTIDASE / IMIDODIPEPTIDASE


Mass: 54661.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: RZPD GERMAN RESOURCE CENTER CDNA CLONE MPMGP800M05547
Organ: FOETAL BRAIN / Plasmid: RZPD CLONE ID PSFEP250H122 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1/PRARE / References: UniProt: P12955, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 991 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPARTICIPATES IN THE PEPTIDE BOND CLEAVAGE INVOLVIND A PROLYL OR HYDROXYPROLYL RESIDUE.

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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: 2.9 Å3/Da / Density % sol: 56.5 %
Description: NATIVE DATA STRUCTURE MODEL BASED ON STARTING MODEL AUTOBUILT BY RESOLVE USING SEMET-MAD DATASET
Crystal growpH: 8.5 / Details: 0.7M NA-CITRATE, 0.01M NA-BORATE PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9004
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2003 / Details: MIRRORS
RadiationMonochromator: SI111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9004 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 103818 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 21.27 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.82→29.51 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.007 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 5189 5 %RANDOM
Rwork0.157 ---
obs0.159 98613 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.82→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7434 0 5 991 8430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217681
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9510395
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73923.159364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.276151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.811562
X-RAY DIFFRACTIONr_chiral_restr0.0980.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23727
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25243
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2794
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.54738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31227627
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42333021
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.054.52764
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.86 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 366
Rwork0.194 6898
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)
10.47090.03380.08930.58640.10060.37810.038-0.0351-0.02320.2026-0.0031-0.0820.04130.0279-0.03490.06490.0094-0.02280.0866-0.0203-0.014290.96534.54395.235
20.9255-0.1461-0.29141.4454-0.05341.0896-0.0144-0.089-0.12030.31130.0206-0.03040.18870.0351-0.00620.1050.0011-0.03090.0689-0.0229-0.051388.09431.193100.607
30.4053-0.004-0.00620.7153-0.14570.46810.03420.0250.0812-0.00710.0184-0.0167-0.0615-0.024-0.05260.01050.02310.02520.0840.00410.007785.25352.81370.803
40.62460.0896-0.13380.5378-0.11610.3275-0.0040.02720.0717-0.02020.04850.1418-0.0212-0.0589-0.0445-0.00570.0231-0.00960.07690.00660.035763.03524.86371.201
50.9088-0.3023-0.05331.3485-0.2620.8355-0.048-0.0328-0.0312-0.010.0191-0.1290.06810.03630.02890.02430.02520.01450.0835-0.01750.03493.53120.80370.26
60.65-0.0295-0.00490.8549-0.0770.388-0.0216-0.0593-0.1224-0.0090.0188-0.08930.09020.01410.00280.01450.04160.00670.0668-0.00480.028189.4832.41474.625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 91
2X-RAY DIFFRACTION2A92 - 194
3X-RAY DIFFRACTION3A195 - 483
4X-RAY DIFFRACTION4B7 - 207
5X-RAY DIFFRACTION5B208 - 256
6X-RAY DIFFRACTION6B257 - 483

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