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- PDB-5g50: Vibrio cholerae scaffolding protein RbmA in complex with magnesium. -

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Basic information

Entry
Database: PDB / ID: 5g50
TitleVibrio cholerae scaffolding protein RbmA in complex with magnesium.
ComponentsRBMA
KeywordsADHESION / BIOFILM / AUTOPROTEOLYSIS
Function / homologyImmunoglobulin-like - #3880 / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesVIBRIO CHOLERAE MJ-1236 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaestre-Reyna, M. / Wu, W.-J. / Lee, C.-C. / Wang, A.H.-J.
CitationJournal: To be Published
Title: Phosphate-Dependent Rbma Autoproteolysis is Involved in Biofilm Dispersal of Vibrio Cholerae
Authors: Maestre-Reyna, M. / Wu, W.-J. / Lee, C.-C. / Wang, A.H.-J.
History
DepositionMay 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: RBMA
B: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4173
Polymers57,3922
Non-polymers241
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-31.1 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.513, 123.513, 100.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2086-

HOH

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Components

#1: Protein RBMA


Mass: 28696.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VIBRIO CHOLERAE SCAFFOLDING PROTEIN RBMA / Source: (gene. exp.) VIBRIO CHOLERAE MJ-1236 (bacteria) / Description: ARTIFICIAL GENE / Variant: SEROTYPE O1 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3LTH7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.68 Å3/Da / Density % sol: 66.62 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M BIS-TRIS, PH 6, 0.2 M NACL, 10 MM MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2015 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.56 Å / Num. obs: 34970 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.16
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BE6

4be6


Resolution: 2.3→46.56 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.699 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23714 1690 4.8 %RANDOM
Rwork0.20157 ---
obs0.20328 33232 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 1 330 3784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023533
X-RAY DIFFRACTIONr_bond_other_d0.0050.023274
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9394806
X-RAY DIFFRACTIONr_angle_other_deg1.13637505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26225.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44515546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.772159
X-RAY DIFFRACTIONr_chiral_restr0.090.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024132
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02805
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_it1.142.8981846
X-RAY DIFFRACTIONr_mcbond_other1.1392.8981845
X-RAY DIFFRACTIONr_mcangle_it1.8114.3442301
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4993.0411687
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 119 -
Rwork0.278 2374 -
obs--97.88 %
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)
13.80530.93330.76192.54750.20332.1547-0.0223-0.3367-0.01170.2489-0.00340.34350.1183-0.39840.02560.21590.02810.05150.2175-0.00740.1218-33.819-11.7586.55
22.0729-0.20540.97670.60560.4371.8599-0.00520.0592-0.27110.0970.03030.25850.3803-0.0815-0.02510.1491-0.00290.01240.13710.00410.1523-31.147-14.312-4.8
312.95756.8565-2.30724.1202-1.21530.8759-0.49-0.107-0.1368-0.22450.23570.2440.3428-0.36190.25440.2446-0.12310.13150.538-0.01290.319-30.281-16.1736.346
43.40090.5919-0.7971.4943-0.00872.1209-0.1254-0.20770.19580.01220.04130.25050.0114-0.18080.08420.18960.0382-0.00340.1966-0.01450.1383-33.077-5.9061.857
51.336-2.07520.49794.83370.03530.5936-0.33610.02240.24090.76980.1693-0.22540.00070.10670.16680.13960.0132-0.0050.1639-0.07440.1633-20.8139.5476.768
60.7711-0.746-0.00921.00910.18991.1845-0.0521-0.06540.21040.03230.0352-0.1641-0.17990.09780.0170.1229-0.00910.01860.1094-0.04960.1355-32.8617.469-1.085
712.86472.2324-1.60071.1465-0.17411.95040.0381-0.12160.02660.1022-0.0253-0.1396-0.07470.173-0.01280.24150.03380.00150.1412-0.03840.2161-29.44710.784-1.885
82.5971-0.6992-1.2151.75610.26371.77930.19570.5560.2661-0.4281-0.21040.2053-0.1588-0.41190.01470.21140.0383-0.00940.17280.03610.1379-36.14714.924-21.089
99.405-5.42413.81923.3738-2.44931.81840.1185-0.31790.53190.23920.08340.0791-0.2866-0.0796-0.20190.4514-0.04880.53940.1751-0.09690.6794-36.05725.075-9.146
1047.71158.533914.52862.19832.66734.4486-1.2035.41253.51940.4690.16740.7601-0.21831.59451.03551.2686-0.7466-0.13091.64220.1820.4272-52.53722.538-25.359
114.24790.0695-0.93441.47090.08391.5241-0.01010.27190.3805-0.2535-0.03380.0586-0.2043-0.20480.04390.18570.00720.01260.14160.01210.0981-33.31913.246-19.275
120.0510.0897-0.29957.0120.64072.27710.03460.03680.0215-0.7039-0.084-0.1358-0.2587-0.16660.04940.1677-0.02380.02270.24480.15660.2373-20.198-3.591-24.542
130.4732-0.01720.28520.64110.0830.8414-0.02420.01760.0506-0.0598-0.01530.03260.090.02780.03950.13570.0010.00360.1339-0.02670.0864-28.972-10.848-15.076
1425.36213.7441-2.76253.7073-1.03882.64930.07850.39880.9114-0.0956-0.07460.048-0.09860.0302-0.00380.22880.0102-0.00980.1376-0.03740.1281-37.658-3.658-16.554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 81
2X-RAY DIFFRACTION2A82 - 107
3X-RAY DIFFRACTION3A108 - 121
4X-RAY DIFFRACTION4A122 - 148
5X-RAY DIFFRACTION5A149 - 169
6X-RAY DIFFRACTION6A170 - 255
7X-RAY DIFFRACTION7A256 - 271
8X-RAY DIFFRACTION8B38 - 89
9X-RAY DIFFRACTION9B90 - 103
10X-RAY DIFFRACTION10B104 - 111
11X-RAY DIFFRACTION11B112 - 152
12X-RAY DIFFRACTION12B153 - 169
13X-RAY DIFFRACTION13B170 - 262
14X-RAY DIFFRACTION14B263 - 271

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