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- PDB-5yz2: the cystathionine-beta-synthase (CBS) domain of magnesium and cob... -

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Basic information

Entry
Database: PDB / ID: 5yz2
Titlethe cystathionine-beta-synthase (CBS) domain of magnesium and cobalt efflux protein CorC in complex with both C2'- and C3'-endo AMP
ComponentsMagnesium and cobalt efflux protein CorC
KeywordsMETAL TRANSPORT / cystathionine-beta-synthase (CBS) domain / magnesium and cobalt efflux protein / AMP binding
Function / homology
Function and homology information


flavin adenine dinucleotide binding / plasma membrane
Similarity search - Function
CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. ...CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Magnesium and cobalt efflux protein CorC
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFeng, N. / Qi, C. / Li, D.F. / Wang, D.C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: The C2'- and C3'-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain.
Authors: Feng, N. / Qi, C. / Hou, Y.J. / Zhang, Y. / Wang, D.C. / Li, D.F.
History
DepositionDec 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Magnesium and cobalt efflux protein CorC
B: Magnesium and cobalt efflux protein CorC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1414
Polymers33,4472
Non-polymers6942
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-17 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.898, 56.290, 54.349
Angle α, β, γ (deg.)90.00, 114.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Magnesium and cobalt efflux protein CorC


Mass: 16723.404 Da / Num. of mol.: 2 / Fragment: Cystathionine-beta-synthase (CBS) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: corC, ybeX, b0658, JW0655 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE78
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 25% PEG 3350, 0.2M Nacl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 29796 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.04
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 6 % / Rmerge(I) obs: 0.766 / Num. unique obs: 2139 / CC1/2: 0.823 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HG0

4hg0


Resolution: 1.75→48.954 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 24.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1996 6.7 %Random selection
Rwork0.2089 ---
obs0.2106 29793 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→48.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 46 155 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032217
X-RAY DIFFRACTIONf_angle_d0.7592987
X-RAY DIFFRACTIONf_dihedral_angle_d12.9311383
X-RAY DIFFRACTIONf_chiral_restr0.048349
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.33481390.28991908X-RAY DIFFRACTION97
1.7938-1.84230.30861450.27551965X-RAY DIFFRACTION100
1.8423-1.89650.30981430.25671993X-RAY DIFFRACTION100
1.8965-1.95770.32571370.24941979X-RAY DIFFRACTION100
1.9577-2.02770.27071500.23231990X-RAY DIFFRACTION100
2.0277-2.10890.25371410.23021988X-RAY DIFFRACTION100
2.1089-2.20480.24311420.22121947X-RAY DIFFRACTION100
2.2048-2.32110.2171430.23292003X-RAY DIFFRACTION100
2.3211-2.46650.28251450.22482003X-RAY DIFFRACTION100
2.4665-2.65690.21361370.22641972X-RAY DIFFRACTION100
2.6569-2.92430.25511440.22282001X-RAY DIFFRACTION99
2.9243-3.34740.23311390.20731995X-RAY DIFFRACTION99
3.3474-4.2170.21461380.18262012X-RAY DIFFRACTION100
4.217-48.97330.21641530.19062041X-RAY DIFFRACTION99
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)
10.0745-0.04170.03530.02360.01250.0395-0.19180.3118-0.4833-0.21960.0488-0.93310.37250.544-0.00250.27210.01070.03440.4130.0570.556534.502810.45616.3374
21.62910.21240.78440.7723-0.4231.6934-0.02350.36860.2122-0.28980.10030.0219-0.4087-0.11980.00240.34390.03890.0020.26290.03480.26888.409115.118-0.9422
31.18360.45060.34460.60010.55930.9527-0.2-0.0155-0.1246-0.0848-0.0363-0.1665-0.12610.15530.00010.29-0.00210.0310.26880.03150.262626.843414.77727.1833
40.25920.03940.02220.0416-0.00750.0046-0.0508-0.50160.08640.07390.2411-0.46460.21060.95620.01380.5875-0.1568-0.11830.8060.0610.672425.16986.020133.7432
50.15390.00870.08090.2381-0.04350.1394-0.2097-0.39780.47561.046-0.11750.0356-0.6855-0.1349-0.00070.4679-0.1035-0.02080.3893-0.03350.345311.601712.297933.429
60.08660.07190.02660.0891-0.05170.00450.2958-0.04160.11580.0647-0.20160.23430.5538-0.7866-0.00050.3541-0.053-0.04030.4305-0.03790.4525-4.640411.546123.8159
70.6298-0.05090.23990.83880.20550.50780.1909-0.27080.65450.7494-0.220.0992-0.3427-0.3207-0.00190.34430.03560.05080.3276-0.00960.3846-1.32613.063722.1711
80.0601-0.12190.13160.0319-0.12560.09190.08010.14650.07220.1415-0.3132-0.01290.18820.1835-0.00020.25220.0191-0.01080.33690.01730.3012-0.30956.534714.2278
90.44930.35-0.70910.7232-0.69120.8191-0.15510.43480.12790.0264-0.0610.1051-0.0479-0.0338-0.02030.2390.0054-0.06930.3598-0.01210.33511.0072.736118.9051
100.4965-0.4981-0.01750.9543-0.20680.3545-0.1626-0.1303-0.40130.0794-0.24340.05120.08460.0397-0.01190.2689-0.00460.01770.3150.06340.270814.2231.250227.8048
110.22970.1487-0.42540.3720.30330.39080.09340.01160.48360.08310.1768-0.04630.0114-0.24340.02780.3296-0.0227-0.00660.28310.00010.409323.000513.447425.0442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 193 )
4X-RAY DIFFRACTION4chain 'B' and (resid 63 through 68 )
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 78 )
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 88 through 112 )
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 150 )
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 174 )
11X-RAY DIFFRACTION11chain 'B' and (resid 175 through 198 )

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