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- PDB-4qtq: Structure of a Xanthomonas Type IV Secretion System related protein -

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Basic information

Entry
Database: PDB / ID: 4qtq
TitleStructure of a Xanthomonas Type IV Secretion System related protein
ComponentsXAC2610 protein
KeywordsHYDROLASE INHIBITOR / Beta-sandwich / calcium binding motif / Beta-propeller fragment / Peptidoglycan hydrolase inhibitor / Immunity protein Xanthomonas
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsSouza, D.P. / Guzzo, C.R. / Farah, C.S.
CitationJournal: Nat Commun / Year: 2015
Title: Bacterial killing via a type IV secretion system.
Authors: Souza, D.P. / Oka, G.U. / Alvarez-Martinez, C.E. / Bisson-Filho, A.W. / Dunger, G. / Hobeika, L. / Cavalcante, N.S. / Alegria, M.C. / Barbosa, L.R. / Salinas, R.K. / Guzzo, C.R. / Farah, C.S.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XAC2610 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3572
Polymers23,3171
Non-polymers401
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.457, 37.695, 43.252
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein XAC2610 protein


Mass: 23317.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: XAC2610, Xanthomonas axonopodis pv. citri / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: Q8PJC5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM BIS-TRIS-HCL PH 5.5, 200 mM AMMONIUM SULPHATE AND 25% (W/V) PEG 3350, VAPOR DIFFUSION , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 25, 2009
RadiationMonochromator: RIGAKU VARIMAX HF OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2→38.78 Å / Num. all: 16929 / Num. obs: 16066 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.1 / % possible all: 89.9

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SHELXDEphasing
REFMAC5.8.0073refinement
d*TREKdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2→38.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.989 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24072 859 5.1 %RANDOM
Rwork0.20013 ---
obs0.20224 16066 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.55 Å2
2---0.37 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 1 180 1771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191643
X-RAY DIFFRACTIONr_bond_other_d0.0010.021517
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.962237
X-RAY DIFFRACTIONr_angle_other_deg0.69533525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21426.26775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01115277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.059154
X-RAY DIFFRACTIONr_chiral_restr0.0720.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_mcbond_it1.6443.211843
X-RAY DIFFRACTIONr_mcbond_other1.6453.207842
X-RAY DIFFRACTIONr_mcangle_it2.844.8021054
X-RAY DIFFRACTIONr_mcangle_other2.844.8061055
X-RAY DIFFRACTIONr_scbond_it1.5073.428800
X-RAY DIFFRACTIONr_scbond_other1.5033.428800
X-RAY DIFFRACTIONr_scangle_other2.5495.0551179
X-RAY DIFFRACTIONr_long_range_B_refined7.57227.111853
X-RAY DIFFRACTIONr_long_range_B_other7.39826.2541792
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 59 -
Rwork0.366 1110 -
obs--88.76 %
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)
17.1844-1.40161.48130.84361.21984.3035-0.43880.33030.00890.7003-0.16840.23241.5442-0.20820.60730.7246-0.18570.17250.14910.09110.280521.9872.4796.937
21.95533.08070.874611.06759.973317.659-0.2057-0.0645-0.02560.39730.1540.28940.20120.54550.05170.21340.03740.09270.09190.03820.142832.4289.43917.619
32.0719-1.4163-2.6412.16491.78863.3921-0.0924-0.1529-0.12330.1777-0.0468-0.12270.11250.12840.13920.0907-0.0250.03460.22380.07070.09928.56516.31315.019
43.4795-4.4538-2.65979.57064.76412.51590.1892-0.2627-0.11120.0826-0.1369-0.2837-0.03370.0163-0.05230.1194-0.02660.02410.14390.03830.159837.95412.1955.755
50.6673-0.7045-0.67060.82111.16684.2596-0.0597-0.1735-0.03810.04160.13190.04140.2806-0.242-0.07220.1755-0.02110.03920.09750.04040.143125.0813.0686.822
63.6563.25439.69093.27619.617528.3361-0.1308-0.35420.48810.2735-0.63650.26250.6884-1.71690.76730.4992-0.228-0.04880.41980.15040.542614.32810.3161.621
74.0302-0.1431-2.69442.10782.72185.11650.22340.2458-0.32210.1946-0.0092-0.26670.123-0.204-0.21430.2491-0.0315-0.02420.05460.05840.284427.0629.298-2.457
82.8797-2.4393-1.78852.26751.80092.35820.09970.036-0.08-0.0549-0.0852-0.08530.089-0.4338-0.01450.1613-0.0120.03340.1569-0.00710.155623.73820.212.369
914.52956.810610.53883.19974.95327.6770.0181.6715-1.1452-0.02530.7881-0.5292-0.07151.2002-0.80610.30750.01870.05460.2457-0.17370.266839.59610.991-6.725
109.0654-3.5910.70621.4478-0.03252.67580.08920.04030.1627-0.0572-0.0232-0.0871-0.1032-0.0683-0.0660.1230.01770.0580.05160.03210.162127.64422.371-5.276
113.9312-4.606-1.45838.41925.43016.97560.06950.0128-0.2765-0.0909-0.120.3380.1336-0.42840.05060.0789-0.04330.00360.09230.01920.091717.39316.513-7.425
1210.8852-4.6307-6.02382.57433.66525.69480.158-0.5482-0.0176-0.0298-0.0559-0.1020.1345-0.2924-0.10210.103-0.0020.01390.27170.00630.051610.33324.134-7.83
1311.39822.85671.78661.48662.80277.4781-0.20890.882-0.3932-0.10890.4542-0.1541-0.21550.8714-0.24530.06250.0130.04820.2459-0.0290.095526.66718.48-15.665
1421.5081-7.4764-12.53743.69675.83149.34140.24580.54050.27970.0724-0.198-0.02660.0953-0.468-0.04770.1047-0.00510.04380.3785-0.00990.02729.58924.888-13.667
1522.3207-1.985-11.72950.50811.57238.26030.17040.80790.5193-0.02440.0335-0.18780.0619-0.9789-0.20390.1244-0.00880.07540.5316-0.1650.14816.79427.719-18.058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 66
2X-RAY DIFFRACTION2A67 - 78
3X-RAY DIFFRACTION3A79 - 100
4X-RAY DIFFRACTION4A101 - 118
5X-RAY DIFFRACTION5A119 - 137
6X-RAY DIFFRACTION6A138 - 144
7X-RAY DIFFRACTION7A145 - 157
8X-RAY DIFFRACTION8A158 - 179
9X-RAY DIFFRACTION9A180 - 187
10X-RAY DIFFRACTION10A188 - 198
11X-RAY DIFFRACTION11A199 - 214
12X-RAY DIFFRACTION12A215 - 228
13X-RAY DIFFRACTION13A229 - 236
14X-RAY DIFFRACTION14A237 - 243
15X-RAY DIFFRACTION15A244 - 267

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