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- PDB-9cy9: Biofilm regulatory protein A from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 9cy9
TitleBiofilm regulatory protein A from Streptococcus mutans
ComponentsBiofilm regulatory protein A
KeywordsLIPID BINDING PROTEIN / LCP family / BrpA / Biofilm / Glucan
Function / homology: / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / cell envelope / Biofilm regulatory protein A
Function and homology information
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsHua, Z. / Hui, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE019452 United States
CitationJournal: To Be Published
Title: Biofilm regulatory protein A from Streptococcus mutans
Authors: Hua, Z. / Hui, W.
History
DepositionAug 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biofilm regulatory protein A


Theoretical massNumber of molelcules
Total (without water)42,1941
Polymers42,1941
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.700, 83.200, 49.400
Angle α, β, γ (deg.)90.000, 99.270, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Biofilm regulatory protein A


Mass: 42193.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Gene: brpA, SMU_410 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DVR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 25291 / % possible obs: 94.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.99 Å2 / CC1/2: 0.995 / Net I/σ(I): 37.894
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 1278 / CC1/2: 0.935

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→34.71 Å / SU ML: 0.1748 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 23.72
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 1968 7.78 %
Rwork0.1835 23316 -
obs0.1867 25284 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.47 Å2
Refinement stepCycle: LAST / Resolution: 1.84→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 0 219 2339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662145
X-RAY DIFFRACTIONf_angle_d0.8622886
X-RAY DIFFRACTIONf_chiral_restr0.0576339
X-RAY DIFFRACTIONf_plane_restr0.0062365
X-RAY DIFFRACTIONf_dihedral_angle_d4.9864294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.2771150.22051373X-RAY DIFFRACTION78.32
1.89-1.940.24451410.22071641X-RAY DIFFRACTION94.04
1.94-20.231360.20061641X-RAY DIFFRACTION94.47
2-2.060.27571440.19811667X-RAY DIFFRACTION94.87
2.06-2.140.23481350.19921607X-RAY DIFFRACTION91.3
2.14-2.220.23181430.1991692X-RAY DIFFRACTION97.76
2.22-2.320.23221420.18491720X-RAY DIFFRACTION98.21
2.32-2.450.24061470.18961723X-RAY DIFFRACTION98.37
2.45-2.60.23921460.19621746X-RAY DIFFRACTION97.98
2.6-2.80.26471410.19871676X-RAY DIFFRACTION96.6
2.8-3.080.25331360.20391601X-RAY DIFFRACTION90.89
3.08-3.520.22651490.18361760X-RAY DIFFRACTION99.48
3.53-4.440.21251470.15551740X-RAY DIFFRACTION98.74
4.44-34.710.18261460.17121729X-RAY DIFFRACTION96.35
Refinement TLS params.Method: refined / Origin x: -7.8184203981 Å / Origin y: -9.59381865055 Å / Origin z: -11.4724469369 Å
111213212223313233
T0.201317218356 Å20.00134715993587 Å2-0.00788771294102 Å2-0.195812200773 Å20.0242839910119 Å2--0.193153178708 Å2
L0.360211809369 °20.0075242981458 °2-0.0799519172452 °2-0.189883770989 °20.062284015078 °2--0.367799543163 °2
S-0.018130851702 Å °0.0704175791264 Å °-0.0205957699843 Å °0.0323952576684 Å °-0.016727702279 Å °0.018256405662 Å °-0.0494170409934 Å °0.0368503191324 Å °-4.97852121187E-6 Å °
Refinement TLS groupSelection details: all

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