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- PDB-2zch: Crystal structure of human prostate specific antigen complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2zch
TitleCrystal structure of human prostate specific antigen complexed with an activating antibody
Components
  • (monoclonal antibody 8G8F5 ...) x 2
  • Prostate-specific antigen
KeywordsIMMUNE SYSTEM / human PSA / kallikrein related peptidases / antibodies / prostate cancer / Glycoprotein / Hydrolase / Polymorphism / Protease / Secreted / Serine protease / Zymogen
Function / homology
Function and homology information


semenogelase / positive regulation of antibacterial peptide production / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / regulation of systemic arterial blood pressure / protein metabolic process / zymogen activation / serine-type peptidase activity / negative regulation of angiogenesis / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...semenogelase / positive regulation of antibacterial peptide production / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / regulation of systemic arterial blood pressure / protein metabolic process / zymogen activation / serine-type peptidase activity / negative regulation of angiogenesis / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endopeptidase activity / serine-type endopeptidase activity / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / PHOSPHATE ION / Prostate-specific antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMenez, R. / Stura, E. / Jolivet-Reynaud, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a ternary complex between human prostate-specific antigen, its substrate acyl intermediate and an activating antibody
Authors: Michel, S. / Muller, B.H. / Bossus, M. / Ducancel, F. / Jolivet-Reynaud, C. / Stura, E.A.
History
DepositionNov 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Prostate-specific antigen
L: monoclonal antibody 8G8F5 Fab
H: monoclonal antibody 8G8F5 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5067
Polymers73,9333
Non-polymers5734
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-45.9 kcal/mol
Surface area30310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.360, 87.360, 236.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody monoclonal antibody 8G8F5 Fab


Mass: 23444.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ascitic fluids / Source: (natural) Mus musculus (house mouse) / Strain: BALB/cjYco
#3: Antibody monoclonal antibody 8G8F5 Fab


Mass: 24366.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ascitic fluids / Source: (natural) Mus musculus (house mouse) / Strain: BALB/cjYco

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Protein / Sugars , 2 types, 3 molecules P

#1: Protein Prostate-specific antigen / PSA / Kallikrein- 3 / Semenogelase / Gamma-seminoprotein / Seminin / P-30 antigen


Mass: 26122.025 Da / Num. of mol.: 1 / Fragment: UNP residues 25-261 / Source method: isolated from a natural source / Details: human seminal fluid / Source: (natural) Homo sapiens (human) / References: UniProt: P07288, semenogelase
#4: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 68 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR CHAIN L AND H DOES NOT CURRENTLY EXIST.

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 14% MPEG 550, 100mM HEPES, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2006
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→78.81 Å / Num. obs: 23506 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.159 / Rsym value: 0.168 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3342 / Rsym value: 0.525 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
MOSFLMdata reduction
PROCESSdata scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L2E, 1RJL

1l2e

1rjl


Resolution: 2.83→78.81 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.856 / SU B: 13.127 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.996 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27033 1168 5.1 %RANDOM
Rwork0.2032 ---
obs0.20652 21615 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.83→78.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 36 66 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225359
X-RAY DIFFRACTIONr_bond_other_d0.0050.024663
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.967311
X-RAY DIFFRACTIONr_angle_other_deg0.973310928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0835678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15724.476210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42415846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8051521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
X-RAY DIFFRACTIONr_nbd_refined0.2270.21083
X-RAY DIFFRACTIONr_nbd_other0.2210.24879
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22558
X-RAY DIFFRACTIONr_nbtor_other0.0970.23105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.25
X-RAY DIFFRACTIONr_mcbond_it1.3991.54231
X-RAY DIFFRACTIONr_mcbond_other0.1091.51378
X-RAY DIFFRACTIONr_mcangle_it1.43325502
X-RAY DIFFRACTIONr_scbond_it2.04332306
X-RAY DIFFRACTIONr_scangle_it3.0724.51809
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 81 -
Rwork0.274 1549 -
obs-1549 100 %

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