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- PDB-1itu: HUMAN RENAL DIPEPTIDASE COMPLEXED WITH CILASTATIN -

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Basic information

Entry
Database: PDB / ID: 1itu
TitleHUMAN RENAL DIPEPTIDASE COMPLEXED WITH CILASTATIN
ComponentsRENAL DIPEPTIDASEMembrane dipeptidase
KeywordsHYDROLASE / DIPEPTIDASE / GLYCOPROTEIN / MEMBRANE-BOUND / ZINC PROTEASE BETA-LACTAMASE / CILASTATIN / COMPLEX (HYDROLASE-INHIBITOR)
Function / homology
Function and homology information


lactam catabolic process / leukotriene D4 catabolic process / membrane dipeptidase / GPI anchor binding / antibiotic metabolic process / LTC4-CYSLTR mediated IL4 production / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / Aflatoxin activation and detoxification ...lactam catabolic process / leukotriene D4 catabolic process / membrane dipeptidase / GPI anchor binding / antibiotic metabolic process / LTC4-CYSLTR mediated IL4 production / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / Aflatoxin activation and detoxification / metallodipeptidase activity / Synthesis of Leukotrienes (LT) and Eoxins (EX) / dipeptidase activity / metalloexopeptidase activity / microvillus membrane / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to nitric oxide / glutathione metabolic process / side of membrane / cellular response to calcium ion / neutrophil chemotaxis / negative regulation of cell migration / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / beta-lactamase activity / beta-lactamase / cellular response to xenobiotic stimulus / apical part of cell / cell junction / inflammatory response / apical plasma membrane / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane
Similarity search - Function
Membrane dipeptidase, active site / Renal dipeptidase active site. / Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CILASTATIN / Dipeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNitanai, Y. / Satow, Y. / Adachi, H. / Tsujimoto, M.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of Human Renal Dipeptidase Involved in beta-Lactam Hydrolysis
Authors: Nitanai, Y. / Satow, Y. / Adachi, H. / Tsujimoto, M.
#1: Journal: J.CRYST.GROWTH / Year: 1996
Title: Crystallization and preliminary X-ray investigation of a glycoprotein, human renal dipeptidase
Authors: Nitanai, Y. / Satow, Y. / Adachi, H. / Tsujimoto, M.
History
DepositionFeb 3, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RENAL DIPEPTIDASE
B: RENAL DIPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,08012
Polymers82,2162
Non-polymers1,86310
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-155 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.179, 79.491, 56.951
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer generated from the dimer in the asymmetric unit.

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Components

#1: Protein RENAL DIPEPTIDASE / Membrane dipeptidase / Microsomal dipeptidase


Mass: 41108.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: renal cortex / Plasmid: PHILD2 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P16444, membrane dipeptidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CIL / CILASTATIN / Cilastatin


Mass: 358.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 8000, HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 5.6 / Details: Nitanai, Y., (1996) J.CRYST.GROWTH, 168, 280.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
27.5 %(w/v)PEG80001droppH5.6
315 %PEG80001reservoirpH5.6

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 30, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 46290 / Num. obs: 46290 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.19 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.274 / % possible all: 84.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 185396

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE DIPEPTIDASE STRUCTURE

Resolution: 2→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4590 10 %RANDOM
Rwork0.185 ---
all0.1909 45937 --
obs0.1898 45648 95.5 %-
Displacement parametersBiso mean: 17.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 92 607 6475
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_dihedral_angle_d22.76
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_mcbond_it1.8741.5
X-RAY DIFFRACTIONx_mcangle_it2.6692
X-RAY DIFFRACTIONx_scbond_it3.0592
X-RAY DIFFRACTIONx_scangle_it4.322.5
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3484 285 10 %
Rwork0.2875 2357 -
obs--82.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION4PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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