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- PDB-4hvl: Structure of a serine protease MycP1, an essential component of t... -

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Basic information

Entry
Database: PDB / ID: 4hvl
TitleStructure of a serine protease MycP1, an essential component of the type VII (ESX-1) secretion system
ComponentsMembrane-anchored mycosin mycp1
KeywordsMEMBRANE PROTEIN / serine protease / subtilisin / mycosin / Rv3883c / protein secretion / subtilisin fold / protease / cell wall
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Type VII secretion system peptidase S8A, mycosin / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Membrane-anchored mycosin mycp1
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKorotkov, K.V. / Evans, T.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Understanding specificity of the mycosin proteases in ESX/type VII secretion by structural and functional analysis.
Authors: Wagner, J.M. / Evans, T.J. / Chen, J. / Zhu, H. / Houben, E.N. / Bitter, W. / Korotkov, K.V.
History
DepositionNov 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: Membrane-anchored mycosin mycp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,51014
Polymers38,6911
Non-polymers81913
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.950, 73.080, 75.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Membrane-anchored mycosin mycp1 / MycP1 protease


Mass: 38690.934 Da / Num. of mol.: 1 / Fragment: UNP residues 19-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / Gene: KEK_05522, MycP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7CDQ2

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Non-polymers , 5 types, 222 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M ZINC ACETATE, 0.1M IMIDAZOLE, 25% 1,2-PROPANEDIOL, 10% GLYCEROL, pH 8.0, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 22-ID21.26
Detector
TypeIDDetectorDate
MAR scanner 300 mm plate1IMAGE PLATEJun 11, 2012
MARMOSAIC 300 mm CCD2CCDJun 11, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.261
ReflectionResolution: 2→47.92 Å / Num. all: 44649 / Num. obs: 44283 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.437 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.41
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.6331.396113300691.5
2.05-2.110.5561.887439316298.1
2.11-2.170.5192.418990314099.3
2.17-2.240.4673.28110783015100
2.24-2.310.394.02112782923100
2.31-2.390.3264.82112042893100
2.39-2.480.2875.46106772747100
2.48-2.580.2416.41103412657100
2.58-2.70.1917.8499872565100
2.7-2.830.169.2693282392100
2.83-2.980.11811.9190112301100
2.98-3.160.09214.5785122176100
3.16-3.380.07317.5480852068100
3.38-3.650.05222.9374371904100
3.65-40.04326.2667491743100
4-4.470.03432.3361891592100
4.47-5.160.03332.8254721406100
5.16-6.330.03332.4246061183100
6.33-8.950.02638.583524914100
8.950.02243.9184249699.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THM

1thm


Resolution: 2→47.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1835 / WRfactor Rwork: 0.1511 / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8879 / SU B: 6.944 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1776 / SU Rfree: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 1208 5.1 %RANDOM
Rwork0.169 ---
all0.1709 23739 --
obs0.1709 23667 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 24.0577 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---1.96 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 31 209 2893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192762
X-RAY DIFFRACTIONr_bond_other_d0.0010.022554
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9593773
X-RAY DIFFRACTIONr_angle_other_deg0.7743.0015857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6255368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81724.299107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92615345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0331517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 87 -
Rwork0.264 1554 -
all-1641 -
obs--96.02 %
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)
10.3442-0.3093-0.57292.3532-0.7591.74640.22790.00060.10090.1388-0.0148-0.0738-0.61830.0146-0.21310.2362-0.02810.06680.113-0.00110.083644.252746.947132.5034
29.67355.8815-0.34354.0271-0.1590.0180.0381-0.2581-0.549-0.015-0.0514-0.4397-0.00660.02460.01340.0650.00690.00110.10790.0060.060141.42221.972821.6662
30.7262-1.0092-0.10944.3923-0.50610.41870.0161-0.0109-0.0009-0.03430.03960.42040.0134-0.1734-0.05570.0014-0.0108-0.00240.12960.00690.107711.691628.277327.6887
41.1242-0.07350.07540.6551-0.15250.3067-0.02080.0664-0.0186-0.07850.02050.0391-0.0056-0.00030.00030.05230.0032-0.01310.0947-0.00170.050826.744932.407918.4647
51.9372-0.3843-0.41131.98140.37991.9537-0.1127-0.22360.04350.24030.1018-0.39430.0280.52180.01090.0855-0.0095-0.01910.1714-0.00820.098246.330131.101926.3105
60.75990.4744-0.29650.5873-0.06451.2242-0.0058-0.09190.00550.02990.0408-0.07990.0660.1302-0.0350.05560.0118-0.00170.0925-0.01250.053840.344639.087228.6691
71.36040.5815-0.42281.0238-0.15641.33820.0649-0.0809-0.0960.0294-0.0439-0.05390.09510.2462-0.0210.06590.0024-0.00720.1211-0.0190.053738.373142.225433.3731
81.25750.30730.96631.01150.60911.83660.0547-0.23430.04940.1385-0.07060.07070.0933-0.11990.01590.04760.00710.01430.1317-0.00280.056431.561437.738145.2616
90.8646-0.005-0.28922.56021.27182.1451-0.0287-0.0471-0.1380.20080.0142-0.03570.3120.16190.01450.064-0.0008-0.02160.0970.01020.081224.285722.398327.5005
100.6358-0.16540.15652.7807-0.39750.6131-0.00050.04320.0970.0603-0.02410.0862-0.0532-0.06560.02460.04180.00070.01060.08710.00940.066221.429541.500929.0474
112.5514-0.73850.5581.1309-2.40885.6649-0.001-0.24060.0112-0.04870.17730.09670.1552-0.3577-0.17630.0734-0.01630.04790.1268-0.06690.135117.98942.001743.5731
127.4349-1.87986.31062.5472-1.77378.4853-0.0185-0.24580.16410.09610.08010.2387-0.2436-0.2696-0.06160.0445-0.00630.05910.0923-0.00550.101316.382341.432737.9088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 41
2X-RAY DIFFRACTION2A42 - 56
3X-RAY DIFFRACTION3A57 - 80
4X-RAY DIFFRACTION4A81 - 148
5X-RAY DIFFRACTION5A149 - 173
6X-RAY DIFFRACTION6A174 - 209
7X-RAY DIFFRACTION7A210 - 244
8X-RAY DIFFRACTION8A245 - 299
9X-RAY DIFFRACTION9A300 - 326
10X-RAY DIFFRACTION10A327 - 362
11X-RAY DIFFRACTION11A363 - 375
12X-RAY DIFFRACTION12A376 - 391

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