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- PDB-2p3w: Crystal Structure of the HtrA3 PDZ Domain Bound to a Phage-Derive... -

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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


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / negative regulation of BMP signaling pathway / 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 / Kazal type serine protease inhibitors / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain ...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 / Kazal type serine protease inhibitors / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)

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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


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

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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: 2.19 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

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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

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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

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