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- PDB-6gjt: Chlamydia protein Pgp3 studied at high resolution in a new crysta... -

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Basic information

Entry
Database: PDB / ID: 6gjt
TitleChlamydia protein Pgp3 studied at high resolution in a new crystal form
ComponentsVirulence plasmid protein pGP3-D
KeywordsCELL ADHESION / Chlamydia / pgp3 / receptor binding.
Function / homology: / Immunodominant antigen Pgp3, helical domain / Immunodominant antigen Pgp3, N-terminal domain / Chlamydia virulence plasmid protein pGP3 / pGP3 C-terminal domain / Pgp3 C-terminal domain / BROMIDE ION / : / Virulence plasmid protein pGP3-D
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHelliwell, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G027005 United Kingdom
CitationJournal: IUCrJ / Year: 2018
Title: Chlamydia protein Pgp3 studied at high resolution in a new crystal form.
Authors: Khurshid, S. / Govada, L. / Wills, G. / McClure, M.O. / Helliwell, J.R. / Chayen, N.E.
History
DepositionMay 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Jan 17, 2024Group: 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 / 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virulence plasmid protein pGP3-D
B: Virulence plasmid protein pGP3-D
C: Virulence plasmid protein pGP3-D
D: Virulence plasmid protein pGP3-D
E: Virulence plasmid protein pGP3-D
F: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,53640
Polymers168,0646
Non-polymers2,47234
Water2,792155
1
A: Virulence plasmid protein pGP3-D
B: Virulence plasmid protein pGP3-D
C: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,26820
Polymers84,0323
Non-polymers1,23617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-66 kcal/mol
Surface area21440 Å2
MethodPISA
2
D: Virulence plasmid protein pGP3-D
E: Virulence plasmid protein pGP3-D
F: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,26820
Polymers84,0323
Non-polymers1,23617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-70 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.410, 108.250, 207.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA2 - 2602 - 260
21GLYGLYPROPROBB2 - 2602 - 260
12SERSERPROPROAA4 - 2604 - 260
22SERSERPROPROCC4 - 2604 - 260
13GLYGLYPROPROAA2 - 2602 - 260
23GLYGLYPROPRODD2 - 2602 - 260
14GLYGLYILEILEAA2 - 2592 - 259
24GLYGLYILEILEEE2 - 2592 - 259
15ASNASNPROPROAA3 - 2603 - 260
25ASNASNPROPROFF3 - 2603 - 260
16SERSERGLNGLNBB4 - 2614 - 261
26SERSERGLNGLNCC4 - 2614 - 261
17GLYGLYGLNGLNBB2 - 2612 - 261
27GLYGLYGLNGLNDD2 - 2612 - 261
18GLYGLYGLNGLNBB2 - 2612 - 261
28GLYGLYGLNGLNEE2 - 2612 - 261
19ASNASNGLNGLNBB3 - 2613 - 261
29ASNASNGLNGLNFF3 - 2613 - 261
110SERSERGLNGLNCC4 - 2614 - 261
210SERSERGLNGLNDD4 - 2614 - 261
111SERSERGLNGLNCC4 - 2614 - 261
211SERSERGLNGLNEE4 - 2614 - 261
112SERSERGLNGLNCC4 - 2614 - 261
212SERSERGLNGLNFF4 - 2614 - 261
113GLYGLYGLNGLNDD2 - 2612 - 261
213GLYGLYGLNGLNEE2 - 2612 - 261
114ASNASNGLNGLNDD3 - 2613 - 261
214ASNASNGLNGLNFF3 - 2613 - 261
115ASNASNGLNGLNEE3 - 2613 - 261
215ASNASNGLNGLNFF3 - 2613 - 261

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Virulence plasmid protein pGP3-D / Proteins P-6/P-7


Mass: 28010.717 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: LGV1 / Plasmid: pCTL1 2A / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE18
#2: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.68 Å3/Da / Density % sol: 54 % / Description: Needle like thick plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: A 7mg per ml Pgp3 stock buffered with 220mM NaCl, 50mM Tris-HCl pH 7.5 and 5mM DTT was screened for suitable crystallization conditions in sitting drop vapour diffusion format using a ...Details: A 7mg per ml Pgp3 stock buffered with 220mM NaCl, 50mM Tris-HCl pH 7.5 and 5mM DTT was screened for suitable crystallization conditions in sitting drop vapour diffusion format using a Mosquito robot (TTP Labtech, UK). A variety of commercially available screens such as Crystal Screen HT, Index HT (Hampton Research, USA), Morpheus and PGA (Molecular Dimensions, UK) were used in 96 well MRC crystallization plates (Molecular Dimensions, UK). All screening trials contained 400 nanolitre drops, each mixed in a 1 to 1 ratio of the protein and the screen solutions. The crystallization trials were incubated at 293K. The different leads obtained from the crystallization screening trials were optimised by determining working phase diagrams as detailed in Saridakis and Chayen (Saridakis & Chayen 2000). Each optimisation trial was also scaled up to 1 microlitre drop volume and set up manually in hanging drops (Qiagen Nextal plates) and in microbatch experiments (Chayen 1999).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.98→45.7 Å / Num. obs: 130981 / % possible obs: 98.1 % / Redundancy: 11.7 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.7
Reflection shellResolution: 1.98→2 Å / Rmerge(I) obs: 1.875 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JDM

4jdm


Resolution: 1.98→42.62 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.899 / SU B: 4.757 / SU ML: 0.13 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 6594 5 %RANDOM
Rwork0.2731 ---
obs0.27407 124208 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.98→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7950 0 34 156 8140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028203
X-RAY DIFFRACTIONr_bond_other_d0.0110.027858
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9711169
X-RAY DIFFRACTIONr_angle_other_deg1.683318056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76451069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86624.646325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.091151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0511542
X-RAY DIFFRACTIONr_chiral_restr0.1170.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219433
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021845
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.683.3984278
X-RAY DIFFRACTIONr_mcbond_other3.6743.3984278
X-RAY DIFFRACTIONr_mcangle_it5.135.0695346
X-RAY DIFFRACTIONr_mcangle_other5.1325.075347
X-RAY DIFFRACTIONr_scbond_it4.293.8463925
X-RAY DIFFRACTIONr_scbond_other4.2893.8463926
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2275.6135824
X-RAY DIFFRACTIONr_long_range_B_refined8.79827.7888528
X-RAY DIFFRACTIONr_long_range_B_other8.79827.7918515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A97270.11
12B97270.11
21A91300.11
22C91300.11
31A96610.09
32D96610.09
41A97390.1
42E97390.1
51A95570.09
52F95570.09
61B90720.11
62C90720.11
71B95800.09
72D95800.09
81B98920.09
82E98920.09
91B94240.1
92F94240.1
101C91160.1
102D91160.1
111C91930.1
112E91930.1
121C92490.09
122F92490.09
131D97640.08
132E97640.08
141D96630.09
142F96630.09
151E95450.09
152F95450.09
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 468 -
Rwork0.393 9106 -
obs--97.97 %

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