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- PDB-1y8t: Crystal Structure of RV0983 from Mycobacterium tuberculosis- Prot... -

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Basic information

Entry
Database: PDB / ID: 1y8t
TitleCrystal Structure of RV0983 from Mycobacterium tuberculosis- Proteolytically active form
Componentshypothetical protein Rv0983Hypothesis
KeywordsUNKNOWN FUNCTION / SERINE PROTEASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


peptidase Do / cellular response to antibiotic / serine-type peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular region / plasma membrane
Similarity search - Function
PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases ...PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease PepD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsPalaninathan, S.K. / MohamedMohaideen, N.N. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Possible role for HtrA homologs in mycobacterium tuberculosis
Authors: Palaninathan, S.K. / MohamedMohaideen, N.N. / Sacchettini, J.C.
History
DepositionDec 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Rv0983
B: hypothetical protein Rv0983
C: hypothetical protein Rv0983


Theoretical massNumber of molelcules
Total (without water)97,1073
Polymers97,1073
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-31 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.584, 89.067, 69.408
Angle α, β, γ (deg.)90.00, 97.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-325-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C
161A
171B
181C
191A
201B
211C
221A
231B
241C
251A
261B
271C
281A
291B
301C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA7 - 267 - 26
21SERSERASPASPBB7 - 257 - 25
31SERSERASPASPCC7 - 257 - 25
42GLUGLUALAALAAA32 - 5532 - 55
52GLUGLUALAALABB32 - 5432 - 54
62GLUGLUALAALACC32 - 5532 - 55
73LYSLYSTHRTHRAA65 - 14465 - 144
83LYSLYSTHRTHRBB65 - 14465 - 144
93LYSLYSTHRTHRCC65 - 14465 - 144
104THRTHRLEULEUAA153 - 190153 - 190
114THRTHRGLYGLYBB153 - 191153 - 191
124THRTHRLEULEUCC153 - 190153 - 190
135GLYGLYASPASPAA200 - 238200 - 238
145GLYGLYASPASPBB200 - 238200 - 238
155GLYGLYASNASNCC200 - 237200 - 237
166ALAALAVALVALAA244 - 250244 - 250
176ALAALAVALVALBB244 - 250244 - 250
186ALAALAVALVALCC244 - 249244 - 249
197ALAALAALAALAAA254 - 256254 - 256
207ALAALAALAALABB254 - 256254 - 256
217ALAALAALAALACC254 - 255254 - 255
228PROPROASPASPAA261 - 271261 - 271
238PROPROASPASPBB261 - 271261 - 271
248PROPROASPASPCC261 - 270261 - 270
259PROPROLEULEUAA273 - 295273 - 295
269PROPROLEULEUBB273 - 295273 - 295
279PROPROALAALACC273 - 294273 - 294
2810GLYGLYALAALAAA312 - 314312 - 314
2910GLYGLYALAALABB312 - 314312 - 314
3010GLYGLYALAALACC312 - 314312 - 314

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Components

#1: Protein hypothetical protein Rv0983 / Hypothesis


Mass: 32368.926 Da / Num. of mol.: 3 / Fragment: SERINE PROTEASE - HtrA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): B121de3 / References: UniProt: O53896
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979, 0.94181, 0.97923
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 30, 2004
RadiationMonochromator: SYNCROTRON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.941811
30.979231
ReflectionResolution: 1.85→76.7 Å / Num. obs: 76977 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.12
Reflection shellResolution: 1.85→1.99 Å / Redundancy: 6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.87 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: CRYSTAL STRUCTURE OF RV1223 (STRUCTURE of RV1223 has been SOLVED at HOME, TO BE SUBMITTED TO PDB SOON)

Resolution: 2→76.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.662 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28027 3078 5.1 %RANDOM
Rwork0.22652 ---
obs0.22931 57235 98.8 %-
all-57235 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.5 Å2
2---0.89 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 2→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 0 318 5749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0225466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1641.9767474
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9965787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93226.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.8715759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2851519
X-RAY DIFFRACTIONr_chiral_restr0.2530.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023925
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.22516
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23505
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.471.54136
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14626327
X-RAY DIFFRACTIONr_scbond_it3.69431510
X-RAY DIFFRACTIONr_scangle_it5.584.51147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1591 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.450.5
2Bmedium positional0.520.5
3Cmedium positional0.540.5
1Amedium thermal2.252
2Bmedium thermal2.052
3Cmedium thermal1.692
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 206 -
Rwork0.321 3925 -
obs--91.68 %
Refinement TLS params.Method: refined / Origin x: 43.6233 Å / Origin y: 43.952 Å / Origin z: 20.1273 Å
111213212223313233
T-0.0494 Å2-0.1006 Å2-0.0067 Å2--0.0481 Å2-0.0196 Å2---0.1481 Å2
L1.326 °20.3262 °2-0.0938 °2-0.7724 °20.0207 °2--0.4857 °2
S-0.1945 Å °0.2054 Å °-0.0017 Å °-0.1298 Å °0.1469 Å °-0.0607 Å °-0.0496 Å °0.0697 Å °0.0477 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 3127 - 312
2X-RAY DIFFRACTION1BB7 - 3127 - 312
3X-RAY DIFFRACTION1CC7 - 3127 - 312

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