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- PDB-7l71: Crystal Structure of the PDZ Domain of the Serine Peptidase HtrA ... -

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Basic information

Entry
Database: PDB / ID: 7l71
TitleCrystal Structure of the PDZ Domain of the Serine Peptidase HtrA from Streptococcus agalactiae.
ComponentsSerine protease
KeywordsPROTEIN BINDING / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Serine Peptidase HtrA / PDZ
Function / homology
Function and homology information


metallopeptidase activity / serine-type endopeptidase activity / plasma membrane
Similarity search - Function
PDZ domain / Peptidase S1C / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesStreptococcus agalactiae A909 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.97 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of the PDZ Domain of the Serine Peptidase HtrA from Streptococcus agalactiae.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4962
Polymers12,4611
Non-polymers351
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.878, 29.330, 35.827
Angle α, β, γ (deg.)90.000, 101.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine protease


Mass: 12460.919 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae A909 (bacteria)
Gene: HtrA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q8DWP1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.83 Å3/Da / Density % sol: 32.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.0 mg/ml, 0.01M Tris pH 8.3;Screen: PACT (D4), 0.1M MMT buffer pH 7.0, 25% (w/v) PEG 1500.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2019 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 0.97→30 Å / Num. obs: 49931 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Rsym value: 0.082 / Χ2: 1.785 / Net I/σ(I): 30.9
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1981 / CC1/2: 0.904 / CC star: 0.974 / Rpim(I) all: 0.304 / Rrim(I) all: 0.846 / Rsym value: 0.787 / Χ2: 1.002 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 0.97→20.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.51 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1501 2525 5.1 %RANDOM
Rwork0.139 ---
obs0.1396 47402 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.68 Å2 / Biso mean: 12.932 Å2 / Biso min: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.08 Å2
2--0.3 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 0.97→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 1 177 989
Biso mean--9.1 23.92 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013899
X-RAY DIFFRACTIONr_bond_other_d0.0010.017903
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6481227
X-RAY DIFFRACTIONr_angle_other_deg0.4051.5892129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.13525.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.42615179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.319152
X-RAY DIFFRACTIONr_chiral_restr0.0730.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.021003
X-RAY DIFFRACTIONr_gen_planes_other0.0570.02147
X-RAY DIFFRACTIONr_rigid_bond_restr1.33631801
LS refinement shellResolution: 0.97→0.995 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 147 -
Rwork0.231 2970 -
all-3117 -
obs--78.67 %
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)
10.6730.1329-0.14510.4188-1.21684.37680.0178-0.1086-0.0391-0.0327-0.0496-0.00860.1822-0.05890.03170.0387-0.0162-0.00820.101-0.01340.06293.954122.696811.7086
26.57173.72582.81483.15961.15693.6516-0.03630.1140.2024-0.0096-0.01160.0789-0.1894-0.11270.04790.0240.019-0.010.02730.00390.02315.877234.5004-1.3129
32.3011-0.2697-0.31051.7213-0.27872.682-0.02760.07020.0435-0.09840.02370.0419-0.0783-0.06920.00390.01740.0046-0.01560.0249-0.01350.023710.25629.13844.7812
42.44421.3338-0.57471.9485-2.91485.7032-0.0181-0.23540.22090.14420.09320.1378-0.3466-0.4395-0.07510.05010.05020.00330.0811-0.02780.05255.824531.862517.8464
51.4701-0.36470.92612.8643-0.7462.60620.05930.0923-0.0778-0.0995-0.06870.01170.20620.10530.00940.02320.0108-0.00870.0084-0.0080.023314.426521.75429.359
63.29961.3817-0.15482.2955-0.54173.68250.0769-0.1482-0.13580.04140.0077-0.01260.2019-0.2024-0.08460.04650.0042-0.02340.03560.00420.05436.545717.028111.9724
71.66080.8724-0.07812.0776-1.26384.58630.041-0.1569-0.07260.0020.04250.12330.0804-0.249-0.08360.0187-0.006-0.00190.03250.01510.036211.761418.225221.7771
82.70890.46970.65613.1794-0.48881.5316-0.02370.09030.09-0.0014-0.02090.0232-0.06240.07210.04450.0207-0.0062-0.01540.00650.00590.013817.070232.24389.0017
95.92083.5836-3.16212.8876-3.07053.89750.0409-0.18640.06580.08710.00660.0602-0.1366-0.1198-0.04760.03740.00730.00060.0324-0.0060.027311.35624.643122.9712
105.4219-0.96144.60523.6723-1.41888.23780.00340.1112-0.0602-0.0941-0.0638-0.2106-0.09960.03120.06040.00580.00280.00390.0431-0.00340.0401-4.10220.730424.621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 311
2X-RAY DIFFRACTION2A312 - 321
3X-RAY DIFFRACTION3A322 - 335
4X-RAY DIFFRACTION4A336 - 348
5X-RAY DIFFRACTION5A349 - 360
6X-RAY DIFFRACTION6A361 - 370
7X-RAY DIFFRACTION7A371 - 380
8X-RAY DIFFRACTION8A381 - 389
9X-RAY DIFFRACTION9A390 - 397
10X-RAY DIFFRACTION10A398 - 403

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