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- PDB-7lzg: CRYSTAL STRUCTURE OF CBS DOMAIN PROTEIN FROM STREPTOCOCCUS PNEUMO... -

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Basic information

Entry
Database: PDB / ID: 7lzg
TitleCRYSTAL STRUCTURE OF CBS DOMAIN PROTEIN FROM STREPTOCOCCUS PNEUMONIAE TIGR4
ComponentsCBS domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Midwest Center for Structural Genomics / PSI-2 / Protein Structure Initiative / MCSG
Function / homologyDomain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / PHOSPHATE ION / CBS domain protein
Function and homology information
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsChang, C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF CBS DOMAIN PROTEIN FROM STREPTOCOCCUS PNEUMONIAE TIGR4
Authors: Chang, C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 9, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionMar 17, 2021ID: 3K6E
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBS domain protein
B: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8714
Polymers35,6812
Non-polymers1902
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-49 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.225, 85.173, 91.591
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CBS domain protein /


Mass: 17840.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1878 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2URI7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.4 M NA/K PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10970 / % possible obs: 99.1 % / Redundancy: 9.4 % / Biso Wilson estimate: 42.91 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.023 / Rrim(I) all: 0.072 / Χ2: 0.903 / Net I/σ(I): 9.7 / Num. measured all: 102673
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.858.61.3395160.7960.4471.4150.88397.4
2.85-2.99.11.1375520.7590.3681.1970.88997.2
2.9-2.969.40.8645330.870.2810.910.89599.8
2.96-3.029.50.7835270.8720.2530.8240.931100
3.02-3.089.60.6265340.9130.2020.6590.93797.8
3.08-3.159.80.5195360.9340.1660.5450.936100
3.15-3.239.70.4125440.9610.1320.4330.92999.5
3.23-3.329.80.3185350.980.1030.3350.89498.9
3.32-3.429.70.2675470.9760.0860.2810.955100
3.42-3.539.80.2025320.990.0650.2120.998.7
3.53-3.659.60.1415540.9930.0460.1480.96100
3.65-3.89.70.1025340.9950.0330.1070.92698.9
3.8-3.979.60.0825490.9950.0270.0870.90999.3
3.97-4.189.60.0625500.9940.020.0650.884100
4.18-4.449.40.0455560.9950.0150.0470.85699.5
4.44-4.799.40.0375560.9970.0120.0390.85299.5
4.79-5.279.40.0365530.9980.0120.0380.87799.6
5.27-6.039.20.0365700.9940.0120.0380.92199.7
6.03-7.598.60.035760.9940.010.0320.8399.7
7.59-5080.0256160.9810.0090.0270.8996.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→45.8 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 819 4.61 %
Rwork0.2304 16957 -
obs0.2321 9836 87.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.05 Å2 / Biso mean: 48.6869 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 2.81→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 10 47 2400
Biso mean--87.32 36.88 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.81-2.990.4202630.31191413147643
2.99-3.220.33481530.30222679283284
3.22-3.540.34541430.27373221336499
3.54-4.050.25161590.218532113370100
4.05-5.110.20491620.189632223384100
5.11-45.80.24791390.21153211335099
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)
10.115-0.0295-0.0910.1945-0.05410.08240.0751-0.045-0.02180.47150.02570.221-0.3314-0.084-0.0170.27280.00720.04790.23160.11890.239615.69657.31270.284
20.09980.1619-0.18160.1753-0.16540.3071-0.25160.0979-0.3087-0.3453-0.0461-0.31050.59960.086-0.0810.1679-0.01760.15090.18090.16410.199825.93744.37461.988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:143 OR RESID 201:201 ) )A-2 - 143
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:143 OR RESID 201:201 ) )A201
3X-RAY DIFFRACTION2( CHAIN B AND RESID -1:151 ) OR ( CHAIN A AND RESID 202:202 )B-1 - 151
4X-RAY DIFFRACTION2( CHAIN B AND RESID -1:151 ) OR ( CHAIN A AND RESID 202:202 )A202

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