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- PDB-3gcd: Structure of the V. cholerae RTX cysteine protease domain in comp... -

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Basic information

Entry
Database: PDB / ID: 3gcd
TitleStructure of the V. cholerae RTX cysteine protease domain in complex with an aza-Leucine peptide inhibitor
ComponentsRTX toxin RtxA
KeywordsTOXIN/INHIBITOR / V. cholerae / repeats-in-toxin / MARTX / cysteine protease / inositol hexakisphosphate / aza-peptide / aza-Leu / TOXIN-INHIBITOR complex
Function / homology
Function and homology information


CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / ligase activity / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament organization / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding ...CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / ligase activity / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament organization / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
MARTX cysteine protease (CPD) domain / : / C-terminal repeat from RTX toxins / : / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain ...MARTX cysteine protease (CPD) domain / : / C-terminal repeat from RTX toxins / : / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
aza-Leu epoxide inhibitor JCP598 / Chem-AZ0 / INOSITOL HEXAKISPHOSPHATE / Multifunctional-autoprocessing repeats-in-toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLupardus, P.J. / Garcia, K.C. / Shen, A. / Bogyo, M.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin.
Authors: Shen, A. / Lupardus, P.J. / Albrow, V.E. / Guzzetta, A. / Powers, J.C. / Garcia, K.C. / Bogyo, M.
History
DepositionFeb 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 14, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.conn_type_id / _struct_conn.id / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RTX toxin RtxA
B: RTX toxin RtxA
C: RTX toxin RtxA
D: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,94316
Polymers90,8404
Non-polymers5,10312
Water2,612145
1
A: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9864
Polymers22,7101
Non-polymers1,2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9864
Polymers22,7101
Non-polymers1,2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9864
Polymers22,7101
Non-polymers1,2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9864
Polymers22,7101
Non-polymers1,2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.560, 65.854, 254.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a single monomer in complex with a single inositol hexakisphosphate molecule and a single Cbz-Leu-Leu-(aza)Leu-epoxide inhibitor

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Components

#1: Protein
RTX toxin RtxA


Mass: 22709.922 Da / Num. of mol.: 4 / Fragment: residues 3442-3650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: V. cholerae 01 biovar eltor str. N16961 / Gene: rtxA, vc1451, VC_1451 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KS12
#2: Chemical
ChemComp-AZ0 / ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 592.724 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H48N4O8 / References: aza-Leu epoxide inhibitor JCP598
#3: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30%PEG3350, 15% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 31246 / % possible obs: 89 % / Redundancy: 4.4 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2112 / % possible all: 61.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3EEB

3eeb


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 22.357 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.823 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26499 1573 5 %RANDOM
Rwork0.21831 ---
obs0.22064 29632 88.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.312 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å2-0 Å2-0 Å2
2---2.56 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 316 145 6677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9689004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0045808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46725.679324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.257151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0031532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024984
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.54036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66826452
X-RAY DIFFRACTIONr_scbond_it1.63732596
X-RAY DIFFRACTIONr_scangle_it2.7494.52552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 79 -
Rwork0.311 1420 -
obs--59.63 %
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)
10.2770.0510.01950.37380.09850.16810.02130.00210.008-0.0012-0.0182-0.00580.0063-0.0259-0.00310.0315-0.00060.0080.00410.00070.0022-7.368919.5629-61.3617
20.59730.1096-0.04010.46140.13110.3467-0.0062-0.0397-0.00640.04980.0178-0.06590.01370.0063-0.01160.0280.0021-0.00850.0042-0.00330.009816.00131.7014-33.1476
30.29740.08530.00660.3774-0.10360.63520.03410.0216-0.02930.03260.07270.0028-0.1125-0.1013-0.10690.05070.02350.01850.02540.01420.0211-3.8283-4.2956-28.281
40.703-0.1096-0.48750.98190.6041.1982-0.0350.07130.0541-0.00160.04250.02980.0480.0931-0.00750.03740.0095-0.00920.03450.00790.0071-3.338732.5114-1.1385
50.0578-0.9294-0.128819.71972.68380.36570.0289-0.0221-0.0018-0.0767-0.04180.0668-0.0142-0.00240.01290.0409-0.0327-0.00130.0441-0.00420.0049-14.031813.9435-50.3917
64.1915.90682.06648.32552.91251.01890.08610.0409-0.28460.12060.0538-0.39950.04210.0191-0.13990.06110.0131-0.00340.0352-0.01680.0262.7807-16.5251-28.4915
72.2607-5.40543.156313.6446-9.810611.52290.0043-0.0027-0.0208-0.00520.03650.0526-0.0208-0.1042-0.04080.0008-0.0017-0.0020.00890.00410.016624.94727.9985-43.1727
80.44571.83660.81287.57053.34881.48280.0721-0.0011-0.0330.3257-0.0055-0.13030.134-0.0029-0.06660.08770.01920.02680.01070.00130.0258-2.409320.02855.6198
90.01570.01140.02770.04620.0290.0532-0.00580.00160.00560.0122-0.0052-0.0078-0.0031-0.00140.0110.03-0.00090.00840.00820.00180.0185-1.515115.7839-42.2193
100.0627-0.4445-0.14553.16351.03070.33830.01770.0108-0.0092-0.0985-0.04480.0553-0.0313-0.02960.02710.0301-0.00340.00230.0765-0.02580.0172-16.370912.7764-67.0759
111.92181.58942.84791.38072.76636.77160.2319-0.0147-0.17750.128-0.0059-0.1423-0.0238-0.0307-0.2260.08020.0105-0.02340.04410.02030.031427.150133.2809-27.4534
122.78313.2678-4.80093.8374-5.6388.2863-0.26990.0915-0.0885-0.33210.1138-0.10410.4973-0.13630.15610.10130.0573-0.00320.1362-0.03690.01215.893926.7611-7.6846
131.3677-0.2339-1.99780.70880.06643.0318-0.01370.03830.0049-0.02010.03420.03140.0293-0.0728-0.02050.0037-0.0018-0.00180.00370.00220.0018-8.9802-9.4903-38.4847
1400000000000000-00.1379-0.0744-0.14380.06710.06580.155129.436930.8868-22.8836
1500000000000000-00.00410.0209-0.0130.1067-0.06630.0412-15.83898.0939-70.6765
1600000000000000-00.1161-0.03550.11560.0108-0.03530.1152-9.083-7.8519-44.1443
1700000000000000-00.088-0.02030.09430.1961-0.10940.141211.66928.3598-8.2811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 999
2X-RAY DIFFRACTION2B1 - 999
3X-RAY DIFFRACTION3C1 - 999
4X-RAY DIFFRACTION4D1 - 999
5X-RAY DIFFRACTION5J1 - 999
6X-RAY DIFFRACTION6K1 - 999
7X-RAY DIFFRACTION7L1 - 999
8X-RAY DIFFRACTION8M1 - 999
9X-RAY DIFFRACTION9I1 - 999
10X-RAY DIFFRACTION10E1 - 999
11X-RAY DIFFRACTION11F1 - 999
12X-RAY DIFFRACTION12G1 - 999
13X-RAY DIFFRACTION13H1 - 999
14X-RAY DIFFRACTION14N1 - 999
15X-RAY DIFFRACTION15P1 - 999
16X-RAY DIFFRACTION16Q1 - 999
17X-RAY DIFFRACTION17R1 - 999

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