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- PDB-3cnr: Crystal Structure of PilZ (XAC1133) from Xanthomonas axonopodis p... -

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Basic information

Entry
Database: PDB / ID: 3cnr
TitleCrystal Structure of PilZ (XAC1133) from Xanthomonas axonopodis pv citri
ComponentsType IV fimbriae assembly protein
KeywordsUNKNOWN FUNCTION / PilZ / Xanthomonas citri / Type IV pilus assembly
Function / homologypredicted glycosyltransferase like domains / PilZ domain / PilZ domain / cyclic-di-GMP binding / Thrombin, subunit H / Beta Barrel / Mainly Beta / Type IV fimbriae assembly protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsGuzzo, C.R. / Farah, C.S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: PILZ protein structure and interactions with PILB and the FIMX EAL domain: implications for control of type IV pilus biogenesis.
Authors: Guzzo, C.R. / Salinas, R.K. / Andrade, M.O. / Farah, C.S.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type IV fimbriae assembly protein
B: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)25,3562
Polymers25,3562
Non-polymers00
Water2,144119
1
A: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)12,6781
Polymers12,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)12,6781
Polymers12,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.125, 62.125, 83.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA9 - 739 - 73
21GLYGLYBB9 - 739 - 73
32ALAALAAA80 - 10580 - 105
42ALAALABB80 - 10580 - 105

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Components

#1: Protein Type IV fimbriae assembly protein


Mass: 12677.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: pilZ / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PND9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.9 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 24% PEG 4000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.978294, 0.978581, 0.953724
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2007
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9782941
20.9785811
30.9537241
ReflectionResolution: 1.85→40 Å / Num. obs: 13687 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.74 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.278 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Tyrosine 22 in both chains A and B do not present electron density for the side chain hydroxyl group. The occupancy of these OH groups were therefore set to zero. Tyrosine codons for this ...Details: Tyrosine 22 in both chains A and B do not present electron density for the side chain hydroxyl group. The occupancy of these OH groups were therefore set to zero. Tyrosine codons for this position were confirmed by sequencing.
RfactorNum. reflection% reflectionSelection details
Rfree0.24345 730 5.1 %RANDOM
Rwork0.19027 ---
obs0.19285 13687 99.77 %-
all-13687 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 119 1552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221470
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5472.0122007
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17323.33348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73915249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.979158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021091
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.2717
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21032
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.5971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16321526
X-RAY DIFFRACTIONr_scbond_it1.8213569
X-RAY DIFFRACTIONr_scangle_it2.434.5474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
357tight positional0.020.05
324medium positional0.640.5
357tight thermal0.190.5
324medium thermal0.672
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 54 -
Rwork0.228 990 -
obs--98.4 %

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