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- PDB-7uxg: Crystal structure of putative serine protease YdgD from Escherich... -

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Basic information

Entry
Database: PDB / ID: 7uxg
TitleCrystal structure of putative serine protease YdgD from Escherichia coli
ComponentsSerine protease
KeywordsHYDROLASE / putative peptidase / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / national institute of allergy and infectious diseases
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / Peptidase S1B / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsStogios, P.J. / Michalska, K. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of putative serine protease YdgD from Escherichia coli
Authors: Stogios, P.J.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease


Theoretical massNumber of molelcules
Total (without water)29,3101
Polymers29,3101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.145, 98.145, 43.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Serine protease


Mass: 29310.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ydgD, ydgD_2, ACU57_22575, AWP93_25095, BANRA_00056, BJI68_03860, BJJ90_13150, BO068_000205, BON73_10185, BON74_16740, BON75_12740, BON77_15735, BON80_06260, BON89_22320, BON93_05710, BON98_ ...Gene: ydgD, ydgD_2, ACU57_22575, AWP93_25095, BANRA_00056, BJI68_03860, BJJ90_13150, BO068_000205, BON73_10185, BON74_16740, BON75_12740, BON77_15735, BON80_06260, BON89_22320, BON93_05710, BON98_16280, BvCmsHHP019_03974, C5N07_00380, CA593_20015, CG692_07775, CG831_003591, D0X26_02230, D3Y67_19900, DAH17_21610, DAH37_02090, DAH50_20815, DTL43_20775, E2119_03170, E2122_01640, E2131_13845, E2135_13145, E4K51_03735, E5P22_00880, E5P23_12110, E5P26_08885, E5P27_01355, E5P28_03650, E5P29_01740, E5P31_00130, E5P32_21155, E5P35_03725, E5P36_13145, E5P40_08615, E5P51_00995, E5S36_00460, E5S51_05780, E5S57_04080, EC1094V2_2155, EC3234A_33c00980, EI021_03345, EIZ93_12015, EL79_2119, EL80_2146, ELT20_01625, ELT41_03415, ELX85_00120, EYV17_14080, EYV18_16275, F2N31_02590, F9V24_02495, FQF29_12205, FTV90_17140, FV293_22055, G4A38_00120, GIB53_01320, GKF89_18985, GKG12_05835, GP979_01705, GQE64_03555, GRW05_00070, HMV95_01680, HNC36_07925, HX136_13140, IH768_09235, IH772_23575, J0541_000620, JNP96_14205, NCTC11126_06494, NCTC13216_04284, NCTC8008_01932, NCTC8500_02732, NCTC9037_02649, NCTC9045_02872, NCTC9706_03853, SAMEA3472044_02664, SAMEA3472067_01513, SAMEA3752557_01274, SAMEA3753106_04780, WP2S18E08_23190
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic
References: UniProt: W8T1B8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 11646 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Net I/σ(I): 1.78
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 16.8 % / Rmerge(I) obs: 1.585 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 584 / CC1/2: 0.755 / Rpim(I) all: 0.392 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.24→42.5 Å / SU ML: 0.4641 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 50.2333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3098 1075 4.8 %RANDOM
Rwork0.2584 21304 --
obs0.2608 11624 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.65 Å2
Refinement stepCycle: LAST / Resolution: 2.24→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 0 0 1814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351860
X-RAY DIFFRACTIONf_angle_d0.75542540
X-RAY DIFFRACTIONf_chiral_restr0.0469283
X-RAY DIFFRACTIONf_plane_restr0.006334
X-RAY DIFFRACTIONf_dihedral_angle_d19.1013669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.340.41961220.45472655X-RAY DIFFRACTION98.97
2.35-2.470.40881120.45192677X-RAY DIFFRACTION99.93
2.47-2.620.47341080.42892719X-RAY DIFFRACTION99.93
2.62-2.820.4411480.4162637X-RAY DIFFRACTION100
2.83-3.110.41731680.4142610X-RAY DIFFRACTION99.96
3.11-3.560.3661400.34472682X-RAY DIFFRACTION100
3.56-4.480.33531250.24252675X-RAY DIFFRACTION100
4.49-42.50.24041520.18032649X-RAY DIFFRACTION99.96
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)
19.114825370891.26573717168-2.840593702725.11152120028-1.831508419296.64483927178-0.2374590598080.1537815883370.9075030766980.644071460383-0.1391255620680.487958479423-1.227031953840.007124944652410.3441119534230.903028585191-0.0134437577803-0.1866041170190.873381799782-0.05399650381431.1614340726239.573976966859.85349548320.923370395963
29.660638206972.53692637092-3.522187058994.138746803740.3115159760027.48964459702-0.488006055444-0.838514928354-2.239179401470.2541851566310.0459075775247-0.7165874077150.2343412192831.214144814860.3688362465090.5570763599690.0475987473763-0.1878389945090.8699014420650.2562741448981.3782408313849.130038661945.02023721590.511793869611
38.47357416501-0.898303913066-2.156632449229.49635831348-0.7126736785745.90946354475-0.297662056194-0.458225706258-0.40954927162-0.109857920756-0.5722089646420.215498819845-0.174799619375-0.4911587480980.8897270066730.370318413765-0.0353594354495-0.0131554892550.641331308450.03984674006590.80789015699330.944370457146.9723213725-0.62647954802
49.552340122043.26299990244-2.089817661888.34551749898-0.6287564666037.27312863034-0.0569167999264-0.6320905078621.956729547370.955554774199-0.348443325571-0.200645846377-1.569755363550.6546800040460.3962099325310.823304860480.010818951961-0.2279442190550.8495572977010.03870070871221.0596729201641.00898958560.8318794559-0.700614300884
58.194135097021.78495417527-4.43542978233.173273745691.455376017284.469074725960.1071879179320.8764136467861.23048820670.9567765061920.816044997142-1.39494319374-0.06248817589110.829890797003-0.8964536391670.805292052585-0.15652638807-0.03791320282140.945111574550.006665162210670.85494665116638.383210303551.7925223602-11.6590190272
67.5697470774-1.54398705371-1.465640339543.95874673767-0.04339213050659.53808509342-0.3915186991580.39368128355-1.23294825749-0.107748282929-0.4913934680070.2643011120450.5946581266870.04875897699270.6958113487840.5310701750360.0532450309298-0.06848193133140.491489606855-0.008086463682130.81648085936230.677347062949.2883300335-1.7026137457
70.9015968028180.453523543284-0.5588227672560.232146262363-0.2920229100280.36883194761.277945280643.826260121564.04815069171-1.65559275497-2.21874180269-2.28061957201-0.1454006979132.321803188491.021493225461.37186613522-0.1228655850020.3684298038222.475118624760.7773970397151.9713772049444.971154501757.7704993699-18.8557348724
87.89824112652-2.593936610514.098575232119.15640113903-0.5653565838313.569374759060.247106691793-0.16238177931-2.0607370242-1.4815040318-0.150480325674-0.1022834225472.458150340240.669593886798-0.09317850841651.077534519840.1382148243480.1879694282330.723621628683-0.1149211270671.5190239256738.984073520337.7514382929-4.42747489387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 35 through 63 )35 - 631 - 29
22chain 'A' and (resid 64 through 151 )64 - 15130 - 117
33chain 'A' and (resid 152 through 186 )152 - 186118 - 152
44chain 'A' and (resid 187 through 202 )187 - 202153 - 168
55chain 'A' and (resid 203 through 225 )203 - 225169 - 191
66chain 'A' and (resid 226 through 242 )226 - 242192 - 208
77chain 'A' and (resid 243 through 254 )243 - 254209 - 220
88chain 'A' and (resid 255 through 273 )255 - 273221 - 239

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