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- PDB-3onr: Crystal structure of the calcium chelating immunodominant antigen... -

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Basic information

Entry
Database: PDB / ID: 3onr
TitleCrystal structure of the calcium chelating immunodominant antigen, calcium dodecin (Rv0379),from Mycobacterium tuberculosis with a novel calcium-binding site
ComponentsPROTEIN TRANSPORT PROTEIN SECE2
KeywordsMETAL BINDING PROTEIN / Calcium dodecin / calcium binding protein / dodecamer / imuuno dominant antigen
Function / homology
Function and homology information


cell wall / metal ion binding / plasma membrane
Similarity search - Function
Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / : / Calcium dodecin
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsArulandu, A. / Sacchettini, J.C.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site.
Authors: Arockiasamy, A. / Aggarwal, A. / Savva, C.G. / Holzenburg, A. / Sacchettini, J.C.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_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: PROTEIN TRANSPORT PROTEIN SECE2
B: PROTEIN TRANSPORT PROTEIN SECE2
C: PROTEIN TRANSPORT PROTEIN SECE2
D: PROTEIN TRANSPORT PROTEIN SECE2
E: PROTEIN TRANSPORT PROTEIN SECE2
F: PROTEIN TRANSPORT PROTEIN SECE2
G: PROTEIN TRANSPORT PROTEIN SECE2
H: PROTEIN TRANSPORT PROTEIN SECE2
I: PROTEIN TRANSPORT PROTEIN SECE2
J: PROTEIN TRANSPORT PROTEIN SECE2
K: PROTEIN TRANSPORT PROTEIN SECE2
L: PROTEIN TRANSPORT PROTEIN SECE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,87731
Polymers96,57912
Non-polymers1,29819
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29800 Å2
ΔGint-159 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.193, 78.446, 152.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PROTEIN TRANSPORT PROTEIN SECE2


Mass: 8048.234 Da / Num. of mol.: 12 / Mutation: A68S, R71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0379, secE2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q6MX43
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging, sitting drop / pH: 8
Details: 1M Sodium Formate, 10mM CaCl2, pH 8.0, vapor diffusion,hanging and sitting drops, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D11.071, 1.072, 1.100
SYNCHROTRONAPS 14-BM-C2
SYNCHROTRONAPS 19-ID3
SYNCHROTRONAPS 23-ID-B4
DetectorDetector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0711
21.0721
31.11
ReflectionResolution: 1.8→76.7 Å / Num. obs: 78271 / Redundancy: 1.9 % / Rsym value: 0.027 / Net I/σ(I): 20.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.894 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3927 5 %RANDOM
Rwork0.1812 ---
obs0.1835 78271 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.88 Å2 / Biso mean: 30.704 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.93 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 43 424 6869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226507
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9638808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55323.487261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.172151133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1951561
X-RAY DIFFRACTIONr_chiral_restr0.1690.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214781
X-RAY DIFFRACTIONr_mcbond_it1.3061.54220
X-RAY DIFFRACTIONr_mcangle_it2.21226802
X-RAY DIFFRACTIONr_scbond_it4.06132287
X-RAY DIFFRACTIONr_scangle_it6.5994.52006
LS refinement shellResolution: 1.8→1.85 Å
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)
12.7944-0.4604-2.02632.12221.04475.1472-0.06040.1321-0.10260.1376-0.01480.18630.1887-0.26340.07520.1147-0.0365-0.01750.1084-0.01690.1051-0.57225.12319.147
24.7554-0.72510.4252.9987-0.50452.78330.01880.258-0.4012-0.1541-0.0575-0.28960.21830.30740.03870.17750.00810.05240.2061-0.06740.113918.38723.0143.948
33.83452.1327-0.99675.1945-0.97342.61940.00810.50440.3922-0.36230.13130.2758-0.2781-0.1339-0.13940.17010.0341-0.01890.2310.03230.06723.77741.9151.927
43.90190.29111.0333.55781.47292.53790.13410.4043-0.2597-0.28390.0452-0.25510.0680.1578-0.17930.17790.02630.12610.2034-0.01610.157133.07737.5854.197
52.2466-0.34571.88493.667-2.22155.6649-0.00540.00320.02440.1251-0.0136-0.4033-0.27950.24710.0190.0802-0.02360.07240.1271-0.01560.164434.43352.25522.618
65.3215-2.0586-1.64932.71791.02232.81770.02890.31090.2363-0.2824-0.01560.0389-0.2437-0.2599-0.01330.1846-0.01450.04340.17970.0610.070517.7155.7035.501
71.4996-1.01190.26915.8171-1.52071.48910.03870.0108-0.13780.0826-0.03040.17310.029-0.0115-0.00830.0579-0.00970.02460.0558-0.01870.0610.93537.29534.817
82.75180.23390.90072.89650.83934.61090.02050.36270.0383-0.4709-0.01670.1181-0.078-0.2118-0.00380.11910.03850.01770.09940.03850.06461.90354.42817.662
93.76310.7239-0.70672.6903-0.09542.46710.0208-0.16210.17380.04070.012-0.2235-0.03250.3977-0.03280.05510.0156-0.01750.0827-0.02250.063918.32254.19535.144
103.5238-1.1795-0.75185.94310.80632.69810.0334-0.16780.30590.2108-0.0043-0.2511-0.11180.1359-0.02910.0396-0.0161-0.04670.09380.03450.155630.74437.19136.485
112.84061.3019-1.45294.5078-0.84073.7424-0.14380.1899-0.1553-0.48770.0254-0.46180.21780.30450.11840.12830.04950.03630.1347-0.00340.155832.25222.56819.377
124.80681.41480.85732.70060.50032.7498-0.0376-0.0652-0.0590.031-0.0840.07040.1287-0.17910.12160.06320.01730.02650.03780.0020.062413.10121.8333.236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 71
2X-RAY DIFFRACTION2B2 - 71
3X-RAY DIFFRACTION3C2 - 71
4X-RAY DIFFRACTION4D2 - 68
5X-RAY DIFFRACTION5E2 - 71
6X-RAY DIFFRACTION6F1 - 71
7X-RAY DIFFRACTION7G1 - 71
8X-RAY DIFFRACTION8H1 - 71
9X-RAY DIFFRACTION9I1 - 71
10X-RAY DIFFRACTION10J2 - 69
11X-RAY DIFFRACTION11K2 - 68
12X-RAY DIFFRACTION12L2 - 71

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