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- PDB-2h1c: Crystal Structure of FitAcB from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 2h1c
TitleCrystal Structure of FitAcB from Neisseria gonorrhoeae
Components(Trafficking protein ...) x 2
KeywordsGENE REGULATION / DNA binding / PIN domain / RHH domain
Function / homology
Function and homology information


migration in host / RNA nuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / DNA binding
Similarity search - Function
PIN domain / VapC family / 5'-nuclease / Arc-type ribbon-helix-helix / Ribbon-helix-helix / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Antitoxin FitA / Toxin FitB / Toxin FitB / Antitoxin FitA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMattison, K. / Wilbur, J.S. / So, M. / Brennan, R.G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs.
Authors: Mattison, K. / Wilbur, J.S. / So, M. / Brennan, R.G.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr2_label_seq_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: Trafficking protein B
B: Trafficking protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5768
Polymers17,2522
Non-polymers3246
Water1,60389
1
A: Trafficking protein B
B: Trafficking protein A
hetero molecules

A: Trafficking protein B
B: Trafficking protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,15216
Polymers34,5044
Non-polymers64812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7540 Å2
ΔGint-147 kcal/mol
Surface area14200 Å2
MethodPISA
2
A: Trafficking protein B
B: Trafficking protein A
hetero molecules

A: Trafficking protein B
B: Trafficking protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,15216
Polymers34,5044
Non-polymers64812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)69.970, 50.700, 48.280
Angle α, β, γ (deg.)90.00, 118.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Trafficking protein ... , 2 types, 2 molecules AB

#1: Protein Trafficking protein B


Mass: 15321.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fitB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9RF91, UniProt: Q5F882*PLUS
#2: Protein/peptide Trafficking protein A


Mass: 1930.253 Da / Num. of mol.: 1 / Fragment: Residues: 46-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fitA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RF92, UniProt: Q5F881*PLUS

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.26 M sodium phosphate/citrate pH 4.7 and 2.0 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.120.9796, 0.9686, 0.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 8, 2005
ADSC QUANTUM 2102CCDMar 8, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal, Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.96861
40.97941
ReflectionResolution: 1.8→39.11 Å / Num. all: 31002 / Num. obs: 13340 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 9.7 / Biso Wilson estimate: 18.8 Å2 / Limit h max: 34 / Limit h min: -38 / Limit k max: 28 / Limit k min: -38 / Limit l max: 26 / Limit l min: 0 / Observed criterion F max: 855178.06 / Observed criterion F min: 6.8 / Rsym value: 0.055
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 13340 / Rsym value: 0.222 / % possible all: 95.3

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCdata collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.11 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1369 10.3 %RANDOM
Rwork0.191 ---
all0.223 13858 --
obs0.223 13340 96.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 56.4884 Å2 / ksol: 0.409027 e/Å3
Displacement parametersBiso max: 64.77 Å2 / Biso mean: 21.76 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å2-1.88 Å2
2--1.11 Å20 Å2
3---2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 17 89 1323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg20.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.2681579.60.24814730.0211716163094.9
1.88-1.980.26317610.60.20814830.021705165997.3
1.98-2.110.2418310.80.18915140.0181740169797.5
2.11-2.270.2551549.20.19415230.0211722167797.4
2.27-2.50.23417410.30.18415100.0181731168497.2
2.5-2.860.21918310.80.17915090.0161746169296.9
2.86-3.60.2317610.60.19914800.0171731165695.7
3.6-39.110.18716610.10.1814790.0151783164592.2

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