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- PDB-5v01: Crystal structure of the competence damage-inducible protein A (C... -

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Basic information

Entry
Database: PDB / ID: 5v01
TitleCrystal structure of the competence damage-inducible protein A (ComA) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
ComponentsCompetence damage-inducible protein A
KeywordsSTRUCTURAL GENOMICS UNKNOWN FUNCTION / cinA family / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyCinA-like / CinA, C-terminal / CinA-like, C-terminal / : / Competence-damaged protein / Maf protein / Alpha-Beta Complex / Alpha Beta / Competence damage-inducible protein A
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBorek, D. / Wawrzak, Z. / Grimshaw, S. / Sandoval, J. / Evdokimova, E. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
CitationJournal: To Be Published
Title: Crystal structure of the competence damage-inducible protein A (ComA) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Authors: Borek, D.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Competence damage-inducible protein A
B: Competence damage-inducible protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,67114
Polymers36,2702
Non-polymers40112
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-117 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.452, 90.433, 44.126
Angle α, β, γ (deg.)90.00, 103.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Competence damage-inducible protein A


Mass: 18135.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: ydeJ, KPN_01597 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A6T8V7
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.2 M NaCl, 0.1 M Ph-Citrate pH4.2, 20% PEG8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 70520 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rsym value: 0.062 / Χ2: 0.94 / Net I/av σ(I): 29.1 / Net I/σ(I): 29.1
Reflection shellResolution: 1.3→1.31 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1759 / CC1/2: 0.653 / Rpim(I) all: 0.447 / Rsym value: 0.876 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A9S

2a9s


Resolution: 1.3→45.22 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.503 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16073 3179 4.9 %RANDOM
Rwork0.12375 ---
obs0.12553 62288 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å20 Å2
2--0.19 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.3→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 19 363 2802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192626
X-RAY DIFFRACTIONr_bond_other_d0.0020.022351
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9193587
X-RAY DIFFRACTIONr_angle_other_deg0.93235425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88123.652115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56615392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4221521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023128
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02577
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_it1.7861.5911399
X-RAY DIFFRACTIONr_mcbond_other1.7861.5921398
X-RAY DIFFRACTIONr_mcangle_it2.282.3931775
X-RAY DIFFRACTIONr_mcangle_other2.282.3921776
X-RAY DIFFRACTIONr_scbond_it3.2561.9711227
X-RAY DIFFRACTIONr_scbond_other3.2491.971226
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0642.8351813
X-RAY DIFFRACTIONr_long_range_B_refined4.79221.4453083
X-RAY DIFFRACTIONr_long_range_B_other4.11120.1752956
X-RAY DIFFRACTIONr_rigid_bond_restr1.4234977
X-RAY DIFFRACTIONr_sphericity_free28.2235236
X-RAY DIFFRACTIONr_sphericity_bonded12.36655062
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 110 -
Rwork0.246 2385 -
obs--46.89 %

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