[English] 日本語
Yorodumi
- PDB-2p3w: Crystal Structure of the HtrA3 PDZ Domain Bound to a Phage-Derive... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p3w
TitleCrystal Structure of the HtrA3 PDZ Domain Bound to a Phage-Derived Ligand (FGRWV)
ComponentsProbable serine protease HTRA3
KeywordsPROTEIN BINDING / PDZ DOMAIN / PHAGE DERIVED HIGH AFFINITY LIGAND
Function / homology
Function and homology information


negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / negative regulation of transforming growth factor beta receptor signaling pathway / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / identical protein binding
Similarity search - Function
Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C ...Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain / Kazal domain / Kazal domain profile. / PDZ domain / Pdz3 Domain / Growth factor receptor cysteine-rich domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Serine protease HTRA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3.
Authors: Runyon, S.T. / Zhang, Y. / Appleton, B.A. / Sazinsky, S.L. / Wu, P. / Pan, B. / Wiesmann, C. / Skelton, N.J. / Sidhu, S.S.
History
DepositionMar 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999 SEQUENCE THE PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable serine protease HTRA3
B: Probable serine protease HTRA3


Theoretical massNumber of molelcules
Total (without water)24,3482
Polymers24,3482
Non-polymers00
Water3,729207
1
A: Probable serine protease HTRA3

A: Probable serine protease HTRA3


Theoretical massNumber of molelcules
Total (without water)24,3482
Polymers24,3482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2
B: Probable serine protease HTRA3

B: Probable serine protease HTRA3


Theoretical massNumber of molelcules
Total (without water)24,3482
Polymers24,3482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)73.001, 73.001, 80.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsChain A forms a dimer by crystollgraphic symmetry symop: y,x,-z (7_555) / Chain B forms a dimer by crystollgraphic symmetry symop: -y,-x,-z+1/2 (8_555)

-
Components

#1: Protein Probable serine protease HTRA3 / High-temperature requirement factor A3 / Pregnancy-related serine protease


Mass: 12173.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA3, PRSP / Production host: Escherichia coli (E. coli)
References: UniProt: P83110, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Bis-Tris, 0.2 M MgCl2, and 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 24442 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.049 / Χ2: 1.027 / Net I/σ(I): 12.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2354 / Rsym value: 0.461 / Χ2: 0.979 / % possible all: 99.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCY

1lcy


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.917 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1224 5 %RANDOM
Rwork0.182 ---
obs0.184 24383 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 207 1839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221676
X-RAY DIFFRACTIONr_bond_other_d0.0010.021589
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9832271
X-RAY DIFFRACTIONr_angle_other_deg0.79133691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62123.69973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86515290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8981516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_nbd_refined0.2040.2230
X-RAY DIFFRACTIONr_nbd_other0.1820.21559
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2780
X-RAY DIFFRACTIONr_nbtor_other0.0780.21063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.218
X-RAY DIFFRACTIONr_mcbond_it2.9752.51383
X-RAY DIFFRACTIONr_mcbond_other0.5852.5445
X-RAY DIFFRACTIONr_mcangle_it3.65351731
X-RAY DIFFRACTIONr_scbond_it3.8892.5671
X-RAY DIFFRACTIONr_scangle_it5.5935537
LS refinement shellResolution: 1.7→1.735 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.256 67 -
Rwork0.216 1316 -
obs-1383 99.28 %
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)
11.8017-0.06880.51351.27780.35912.21060.04530.24910.053-0.2446-0.09260.0065-0.04170.09090.0473-0.03980.03620.0047-0.04370.0061-0.04743.08920.3847-4.7268
22.6302-1.758-4.33837.344810.102515.66480.04670.01240.3029-0.19210.2019-0.3604-0.08570.1005-0.2487-0.00670.0522-0.0244-0.0471-0.02740.001817.192113.4295.4737
32.34310.2977-0.20441.5638-0.84072.33450.1066-0.33240.03830.2602-0.06490.0052-0.16080.0607-0.0417-0.0457-0.02590.0075-0.03930.0008-0.052-2.059620.257623.913
40.18680.9374-1.98914.7044-9.982121.1804-0.18360.27870.2570.13950.32690.4483-0.3846-0.4893-0.14330.0316-0.04620.0118-0.05180.01790.0432-15.373811.679814.5764
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA350 - 4541 - 105
22AA455 - 461106 - 112
33BB350 - 4541 - 105
44BB455 - 461106 - 112

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more