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- PDB-6gs8: Crystal structure of SmbA in complex with c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 6gs8
TitleCrystal structure of SmbA in complex with c-di-GMP
ComponentsUncharacterized protein
KeywordsSIGNALING PROTEIN / c-di-GMP receptor / ppGpp / second messenger / TIM barrel
Function / homologyNADP-dependent oxidoreductase domain superfamily / nucleotide binding / metal ion binding / Chem-C2E / NADP-dependent oxidoreductase domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-138414 Switzerland
CitationJournal: Nat Microbiol / Year: 2021
Title: Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus
Authors: Shyp, V. / Dubey, B.N. / Bohm, R. / Hartl, J. / Nesper, J. / Vorholt, J.A. / Hiller, S. / Schirmer, T. / Jenal, U.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_gene_src_variant ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_gene_src_variant / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_atom_id_1 / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_standard_deviation / _pdbx_validate_rmsd_bond.bond_target_value / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_rmsd_bond.linker_flag / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr_ncs.pdbx_number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_number_measured_all / _reflns.pdbx_redundancy / _reflns.pdbx_scaling_rejects / _reflns.percent_possible_obs / _software.version / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_ins_code
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 10, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.2Jul 20, 2022Group: Advisory / Database references
Category: citation / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,94024
Polymers204,5106
Non-polymers8,43118
Water54030
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers34,0851
Non-polymers1,4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers34,0851
Non-polymers1,4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers34,0851
Non-polymers1,4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers34,0851
Non-polymers1,4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers34,0851
Non-polymers1,4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers34,0851
Non-polymers1,4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.910, 87.420, 130.270
Angle α, β, γ (deg.)90.000, 119.480, 90.000
Int Tables number4
Space group name H-MP1211
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 307
2010B1 - 307
1020A1 - 289
2020C1 - 289
1030A1 - 289
2030D1 - 289
1040A1 - 289
2040E1 - 289
1050A1 - 289
2050F1 - 289
1060B1 - 289
2060C1 - 289
1070B1 - 289
2070D1 - 289
1080B1 - 289
2080E1 - 289
1090B1 - 289
2090F1 - 289
10100C1 - 290
20100D1 - 290
10110C1 - 290
20110E1 - 290
10120C1 - 290
20120F1 - 290
10130D1 - 290
20130E1 - 290
10140D1 - 290
20140F1 - 290
10150E1 - 290
20150F1 - 290

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
Uncharacterized protein


Mass: 34084.941 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Gene: CC_2504 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A5E6
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.15 M potassium thiocyanate, 0.1M Tris pH 8.5, 13% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 2.8→29.57 Å / Num. obs: 58051 / % possible obs: 93.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 22.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.772.8350.9721.17262211008092500.6181.18191.8
2.77-2.843.190.8011.6431147982497630.6980.95899.4
2.84-2.923.5750.6412.3133879951894760.7920.75499.6
2.92-3.013.5770.4743.1133013927392300.8750.55899.5
3.01-3.113.5230.3694.0531323894888900.9030.43699.4
3.11-3.223.3870.2675.4229197866686200.9470.31799.5
3.22-3.343.5110.1768.3529313838883500.9770.20899.5
3.34-3.483.2580.1349.8915845803048630.9860.1660.6
3.48-3.633.6060.10413.4427802773777100.990.12299.7
3.63-3.813.3550.07116.7716723739849840.9940.08567.4
3.81-4.023.3390.05919.1216827701250400.9960.07171.9
4.02-4.263.4670.04723.0622814662265810.9980.05599.4
4.26-4.563.5930.03827.6122427628162420.9980.04599.4
4.56-4.923.540.03230.3720370578357550.9990.03899.5
4.92-5.393.4270.03230.4718288538053360.9980.03899.2
5.39-6.033.5080.03130.6916731480347690.9990.03799.3
6.03-6.963.5270.02933.5214854424642110.9990.03499.2
6.96-8.523.3340.0234111923363035760.9990.02798.5
8.52-12.053.5020.01951.929668280227610.9990.02398.5
12.05-303.3340.02154.424934151714800.9990.02597.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 37.933 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1747 3.1 %RANDOM
Rwork0.2186 ---
obs0.2201 55146 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.3 Å2 / Biso mean: 77.143 Å2 / Biso min: 38.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.03 Å2
2---0.89 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 2.8→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13522 0 466 30 14018
Biso mean--56.4 58.44 -
Num. residues----1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01314314
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712964
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.6519538
X-RAY DIFFRACTIONr_angle_other_deg1.3651.57729918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98851724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4420.647834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49152166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2615154
X-RAY DIFFRACTIONr_chiral_restr0.090.21832
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216146
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023196
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A91190.08
12B91190.08
21A85800.08
22C85800.08
31A86400.06
32D86400.06
41A86580.06
42E86580.06
51A85950.07
52F85950.07
61B85800.07
62C85800.07
71B86640.06
72D86640.06
81B86990.06
82E86990.06
91B86000.06
92F86000.06
101C85870.08
102D85870.08
111C86170.08
112E86170.08
121C85320.08
122F85320.08
131D86530.07
132E86530.07
141D85770.07
142F85770.07
151E85960.07
152F85960.07
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 119 -
Rwork0.371 4051 -
all-4170 -
obs--92.71 %
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)
14.08750.13470.33731.72030.24871.4772-0.1317-0.44280.3219-0.00530.05310.03590.0463-0.07250.07870.16780.04260.0070.073-0.05140.052392.381429.965264.7689
24.2523-0.33470.65771.7782-0.27961.81410.01010.05470.0266-0.0014-0.06050.0355-0.0312-0.10660.05040.2256-0.08190.02550.1025-0.02140.0064112.94227.322527.0599
33.0079-0.26650.27891.817-0.82453.1726-0.03420.24170.34850.01840.0290.0767-0.2273-0.52570.00510.11310.04610.02850.12930.02220.064992.369230.9273-8.9913
42.7761-0.07340.64732.34591.0024.88540.0267-0.02690.1853-0.09880.0751-0.2-0.04490.6453-0.10190.07170.00130.03240.2244-0.05730.050749.504335.309-12.108
52.9104-0.0479-0.92752.3129-0.06533.83280.2095-0.4866-0.13860.06260.07060.022-0.0216-0.0425-0.28020.0905-0.0155-0.00020.10430.04570.038929.012631.517326.3408
61.98560.4028-1.93741.4431-0.7585.4232-0.06330.4074-0.0441-0.030600.0977-0.40750.11380.06330.0943-0.08790.03030.3610.130.175648.198531.522967.5646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 504
2X-RAY DIFFRACTION2B1 - 504
3X-RAY DIFFRACTION3C1 - 504
4X-RAY DIFFRACTION4D1 - 504
5X-RAY DIFFRACTION5E1 - 504
6X-RAY DIFFRACTION6F1 - 504

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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