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- PDB-3mhz: 1.7A structure of 2-fluorohistidine labeled Protective Antigen -

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Basic information

Entry
Database: PDB / ID: 3mhz
Title1.7A structure of 2-fluorohistidine labeled Protective Antigen
ComponentsProtective antigen
KeywordsTOXIN / anthrax / 2-fluorohistidine / pore / histidine / receptor / hydrogen bonding
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding ...positive regulation of apoptotic process in another organism / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane / metal ion binding
Similarity search - Function
Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain ...Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Ubiquitin-like (UB roll) / Jelly Rolls / Roll / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct Replacement / molecular replacement / Resolution: 1.7 Å
AuthorsLovell, S. / Battaile, K.P. / Wimalasena, D.S. / Janowiak, B.E. / Miyagi, M. / Sun, J. / Hajduch, J. / Pooput, C. / Kirk, K.L. / Bann, J.G.
CitationJournal: Biochemistry / Year: 2010
Title: Evidence that histidine protonation of receptor-bound anthrax protective antigen is a trigger for pore formation.
Authors: Wimalasena, D.S. / Janowiak, B.E. / Lovell, S. / Miyagi, M. / Sun, J. / Zhou, H. / Hajduch, J. / Pooput, C. / Kirk, K.L. / Battaile, K.P. / Bann, J.G.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_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_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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 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: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2234
Polymers82,9491
Non-polymers2743
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.368, 93.975, 119.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protective antigen / PA / PA-83 / PA83 / Anthrax toxins translocating protein / Protective antigen PA-20 / PA20 / ...PA / PA-83 / PA83 / Anthrax toxins translocating protein / Protective antigen PA-20 / PA20 / Protective antigen PA-63 / PA63


Mass: 82948.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA, pag, pXO1-110, BXA0164, GBAA_pXO1_0164 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): UTH780 / References: UniProt: P13423
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2
Details: 30% PEG 400, 0.1M Tris, pH 8.2, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 88352 / Num. obs: 88352 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.093 / Χ2: 2.148 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.897 / Num. unique all: 7898 / Χ2: 0.728 / % possible all: 89.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Direct Replacement
Starting model: A lower resolution structure was initially solved from in-house diffraction data by molecular replacement using 1ACC as the starting model. The resulting model was then refined ...Starting model: A lower resolution structure was initially solved from in-house diffraction data by molecular replacement using 1ACC as the starting model. The resulting model was then refined against the high resolution synchrotron data.

1acc


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2217 4400 5.027 %
Rwork0.1917 --
all-87519 -
obs-87519 98.669 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 27.856 Å2
Baniso -1Baniso -2Baniso -3
1--1.809 Å20 Å20 Å2
2---0.604 Å20 Å2
3---2.413 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 15 400 5696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225414
X-RAY DIFFRACTIONr_bond_other_d0.0010.023577
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9747358
X-RAY DIFFRACTIONr_angle_other_deg0.95638804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15525.804255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97215.037935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0721522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021006
X-RAY DIFFRACTIONr_nbd_refined0.2090.2914
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2323
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.218
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0370.21
X-RAY DIFFRACTIONr_mcbond_it0.911.53375
X-RAY DIFFRACTIONr_mcbond_other0.2821.51354
X-RAY DIFFRACTIONr_mcangle_it1.58325489
X-RAY DIFFRACTIONr_mcangle_other0.71624480
X-RAY DIFFRACTIONr_scbond_it2.45232039
X-RAY DIFFRACTIONr_scbond_other0.49932223
X-RAY DIFFRACTIONr_scangle_it3.8524.51862
X-RAY DIFFRACTIONr_scangle_other1.8664.54324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7440.2992840.2415458650388.298
1.744-1.7920.2673120.2235770629096.693
1.792-1.8440.2623240.2225849617899.919
1.844-1.90.2512900.2125667596099.95
1.9-1.9630.2272980.195493579399.965
1.963-2.0310.2242980.19253005598100
2.031-2.1080.2412820.19151565438100
2.108-2.1940.2112400.1854952519399.981
2.194-2.2910.2332460.1874802505699.842
2.291-2.4030.2462170.1834540476899.769
2.403-2.5320.2782270.1964348458499.804
2.532-2.6860.2232200.2094101433699.654
2.686-2.870.2372100.2113849408399.412
2.87-3.10.2271830.2023621382399.503
3.1-3.3940.2171690.1923357353099.887
3.394-3.7930.1841760.1793034321199.969
3.793-4.3750.1941460.1622687283999.789
4.375-5.3480.1891260.162311244199.836
5.348-7.520.2091040.2061818192399.948
7.52-500.234480.2311006115391.414
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)
11.87590.5137-2.16071.2234-1.82125.1534-0.1781-0.0835-0.09330.20820.09210.11210.2801-0.37110.0860.1916-0.04870.05870.1963-0.02830.1073-39.688111.7589-5.0833
24.0190.1325-1.20270.41040.02250.6804-0.11860.0105-0.27380.01090.0388-0.13260.08030.10040.07980.0801-0.0091-0.00030.0512-0.00790.05864.592715.5154-26.3954
31.4109-0.1192-0.19210.78410.15870.3543-0.03590.06390.07920.04110.0320.011-0.0152-0.02440.00380.0755-0.0181-0.00390.05210.00650.0055-10.269826.014-27.0276
43.80850.16710.49943.21320.83981.5755-0.0455-0.25260.11230.27280.0685-0.19830.04850.1073-0.02310.0948-0.0006-0.02220.074-0.00430.061320.616344.4525-22.5799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA15 - 228
2X-RAY DIFFRACTION2ALLA229 - 407
3X-RAY DIFFRACTION3ALLA408 - 606
4X-RAY DIFFRACTION4ALLA607 - 734

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