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- PDB-2z9i: Crystal structure of RV0983 from Mycobacterium tuberculosis- Prot... -

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Basic information

Entry
Database: PDB / ID: 2z9i
TitleCrystal structure of RV0983 from Mycobacterium tuberculosis- Proteolytically active form
Components
  • GATV
  • PROBABLE SERINE PROTEASE PEPD
  • SVEQV
KeywordsHYDROLASE / SERINE PROTEASE / HtrA
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 ...: / 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.
CitationJournal: Biochemistry / Year: 2008
Title: Structure and function of the virulence-associated high-temperature requirement A of Mycobacterium tuberculosis
Authors: Mohamedmohaideen, N.N. / Palaninathan, S.K. / Morin, P.M. / Williams, B.J. / Braunstein, M. / Tichy, S.E. / Locker, J. / Russell, D.H. / Jacobs, W.R. / Sacchettini, J.C.
History
DepositionSep 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PROBABLE SERINE PROTEASE PEPD
B: PROBABLE SERINE PROTEASE PEPD
C: PROBABLE SERINE PROTEASE PEPD
D: SVEQV
E: SVEQV
F: SVEQV
G: GATV
H: GATV
I: GATV


Theoretical massNumber of molelcules
Total (without water)99,8289
Polymers99,8289
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-46 kcal/mol
Surface area30920 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41
51
61
71
81
91
101
111
121
131
141
151

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTHRTHR6AA11 - 2411 - 24
21VALVALTHRTHR6BB11 - 2411 - 24
31VALVALTHRTHR6CC11 - 2411 - 24
42GLUGLUALAALA6AA32 - 5232 - 52
52GLUGLUALAALA6BB32 - 5232 - 52
62GLUGLUALAALA6CC32 - 5232 - 52
73THRTHRVALVAL6AA66 - 14266 - 142
83THRTHRVALVAL6BB66 - 14266 - 142
93THRTHRVALVAL6CC66 - 14266 - 142
104VALVALALAALA6AA154 - 188154 - 188
114VALVALALAALA6BB154 - 188154 - 188
124VALVALALAALA6CC154 - 188154 - 188
135GLYGLYHISHIS1AA200 - 228200 - 228
145GLYGLYHISHIS1BB200 - 228200 - 228
155GLYGLYHISHIS1CC200 - 228200 - 228

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Components

#1: Protein PROBABLE SERINE PROTEASE PEPD / SERINE PROTEINASE / MTB32B


Mass: 32368.926 Da / Num. of mol.: 3 / Fragment: residues in database 149-464 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
References: UniProt: O53896, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide SVEQV


Mass: 560.597 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: autolytic products / Source: (natural) Mycobacterium tuberculosis (bacteria)
#3: Protein/peptide GATV


Mass: 346.379 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: autolytic products / Source: (natural) Mycobacterium tuberculosis (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 7mg/ml protein (in 50mM Tris-HCl, 1mM dithiothreitol (DTT) (pH 7.0)), 0.1M sodium acetate (pH 4.6), 0.1M cadmium chloride, 30% PEG 400 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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. all: 76977 / Num. obs: 76977 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / 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
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.593 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.193 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 3078 5.1 %RANDOM
Rwork0.22505 ---
obs0.22765 57235 98.81 %-
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: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.47 Å2
2---0.8 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 0 327 5920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225622
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9797659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77326.291151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46915792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9341520
X-RAY DIFFRACTIONr_chiral_restr0.1080.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024050
X-RAY DIFFRACTIONr_nbd_refined0.2340.22595
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2411
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.27
X-RAY DIFFRACTIONr_mcbond_it1.91334142
X-RAY DIFFRACTIONr_mcangle_it3.17556451
X-RAY DIFFRACTIONr_scbond_it5.23871562
X-RAY DIFFRACTIONr_scangle_it8.083111201
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A191tight positional0.10.05
2B191tight positional0.180.05
3C191tight positional0.10.05
1A1000loose positional0.385
2B1000loose positional0.375
3C1000loose positional0.475
1A191tight thermal0.160.5
2B191tight thermal0.180.5
3C191tight thermal0.180.5
1A1000loose thermal2.7110
2B1000loose thermal3.4510
3C1000loose thermal3.7410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 206 -
Rwork0.344 3923 -
obs--91.67 %

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