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- PDB-2r2a: Crystal structure of N-terminal domain of zonular occludens toxin... -

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Basic information

Entry
Database: PDB / ID: 2r2a
TitleCrystal structure of N-terminal domain of zonular occludens toxin from Neisseria meningitidis
ComponentsUncharacterized protein
KeywordsTOXIN / Zonular occludens toxin / structural genomics / APC84050.2 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyZona occludens toxin, N-terminal / Zonular occludens toxin (Zot) / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / membrane / Alpha Beta / Zona occludens toxin N-terminal domain-containing protein
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsOsipiuk, J. / Patterson, S. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of N-terminal domain of zonular occludens toxin from Neisseria meningitidis.
Authors: Osipiuk, J. / Patterson, S. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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 / struct_conn / 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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1984
Polymers46,0062
Non-polymers1922
Water4,900272
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0992
Polymers23,0031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.976, 48.258, 95.894
Angle α, β, γ (deg.)90.00, 134.31, 90.00
Int Tables number5
Space group name H-MC121
DetailsAuthors state that the biological unit of this protein is unknown.

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Components

#1: Protein Uncharacterized protein


Mass: 23003.057 Da / Num. of mol.: 2 / Fragment: N-terminal domain: Residues 1-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Species: Neisseria meningitidis / Strain: MC58 / Serogroup B / Gene: NMB1551, NMB1626 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JRY6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium sulfate, 0.1M Sodium citrate, 20% PEG 3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.82→34.4 Å / Num. all: 38209 / Num. obs: 38209 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 28.7
Reflection shellResolution: 1.82→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2923 / % possible all: 74.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→34.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.407 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1931 5.1 %RANDOM
Rwork0.1757 ---
all0.1777 36244 --
obs0.1777 36244 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.803 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å21.66 Å2
2---1.24 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.82→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 10 272 3327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223269
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9654444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04524.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8561516
X-RAY DIFFRACTIONr_chiral_restr0.1220.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022412
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21522
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22192
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0911.52072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56423256
X-RAY DIFFRACTIONr_scbond_it2.36831396
X-RAY DIFFRACTIONr_scangle_it3.4554.51170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 109 -
Rwork0.256 1939 -
obs-2048 70.6 %
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)
11.85-1.54631.43851.4309-1.13552.1759-0.0292-0.0327-0.1121-0.13650.01270.1374-0.0873-0.06070.01650.0435-0.0002-0.05670.01580.01110.055921.025421.554258.6279
22.5759-1.5718-0.14832.52970.48680.80660.26020.2972-0.5296-0.5521-0.24260.4217-0.11650.0182-0.01760.11130.0396-0.15290.032-0.06760.093523.7048.546350.6143
32.2611-1.1499-1.06645.30721.06722.7155-0.0431-0.22780.08360.01830.0965-0.1496-0.20480.1774-0.0534-0.0025-0.0147-0.00050.03920.0230.056735.116518.445265.0159
42.64010.9076-0.28712.11750.38541.61220.1661-0.25590.23080.1188-0.02780.1161-0.1971-0.1445-0.1384-0.03160.0150.01320.01480.04860.044325.475421.901168.8477
52.7525-1.0065-2.20690.95731.84483.59720.0604-0.04810.18520.10070.06930.1140.10810.1166-0.12970.08110.00570.0907-0.01660.00640.0763-9.184522.162948.2792
62.152-0.449-0.7283.97112.90313.9389-0.351-0.0109-0.18731.094-0.12270.76541.122-0.09740.47370.3237-0.04370.3466-0.11570.00740.1506-16.25596.985648.6335
72.3128-1.8786-1.15222.99571.99912.94-0.06250.1954-0.08660.2597-0.11620.63750.3318-0.31260.17880.0189-0.05570.1150.02860.00810.1808-17.235412.907238.8032
82.11541.09241.51985.20050.96742.8308-0.13970.02640.11690.16350.0993-0.09390.01030.26580.04040.03910.02480.01050.05150.0092-0.0038-1.596520.884137.7345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 364 - 39
2X-RAY DIFFRACTION2AA37 - 13440 - 137
3X-RAY DIFFRACTION3AA135 - 166138 - 169
4X-RAY DIFFRACTION4AA167 - 191170 - 194
5X-RAY DIFFRACTION5BB0 - 363 - 39
6X-RAY DIFFRACTION6BB37 - 10940 - 112
7X-RAY DIFFRACTION7BB110 - 137113 - 140
8X-RAY DIFFRACTION8BB138 - 190141 - 193

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