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- PDB-3kxr: Structure of the cystathionine beta-synthase pair domain of the p... -

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Basic information

Entry
Database: PDB / ID: 3kxr
TitleStructure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.
ComponentsMagnesium transporter, putative
KeywordsTRANSPORT PROTEIN / cystathionine beta-synthase / Mg2+ transporter / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
Pheromone ER-1 - #50 / : / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / Pheromone ER-1 / CBS-domain ...Pheromone ER-1 - #50 / : / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / Pheromone ER-1 / CBS-domain / CBS-domain / CBS domain / CBS domain / CBS domain profile. / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Magnesium transporter MgtE family
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsFratczak, Z. / Zimmerman, M.D. / Chruszcz, M. / Cymborowski, M. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.
Authors: Fratczak, Z. / Zimmerman, M.D. / Chruszcz, M. / Cymborowski, M. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Magnesium transporter, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8243
Polymers23,7531
Non-polymers712
Water54030
1
A: Magnesium transporter, putative
hetero molecules

A: Magnesium transporter, putative
hetero molecules

A: Magnesium transporter, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4719
Polymers71,2583
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6130 Å2
ΔGint-79 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.596, 103.596, 134.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Magnesium transporter, putative /


Mass: 23752.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: SO_1565 / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8EGN5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG3350 25%,di-Na-Tartrate 0.2M,Tris0.1M pH8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2009 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 10867 / Num. obs: 10867 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.5 % / Biso Wilson estimate: 61.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 57.071
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 18.3 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 3.6 / Num. unique all: 537 / Rsym value: 0.878 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
CCP4model building
REFMAC5.5.0072refinement
Cootmodel building
HKL-3000data reduction
HKL-2000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 15.798 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.253 / ESU R Free: 0.206
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.228 517 4.8 %RANDOM
Rwork0.19 ---
all0.191 10835 --
obs0.191 10835 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0.93 Å20 Å2
2---1.86 Å20 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 2 30 1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221388
X-RAY DIFFRACTIONr_bond_other_d0.0010.02926
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9631882
X-RAY DIFFRACTIONr_angle_other_deg0.90632251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85824.38473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64715238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.581511
X-RAY DIFFRACTIONr_chiral_restr0.080.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02283
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_it0.6951.5854
X-RAY DIFFRACTIONr_mcbond_other0.1271.5341
X-RAY DIFFRACTIONr_mcangle_it1.41421372
X-RAY DIFFRACTIONr_scbond_it2.6033534
X-RAY DIFFRACTIONr_scangle_it4.1474.5510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 36 -
Rwork0.269 722 -
obs--98.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.7321-0.87431.85381.7970.04220.77230.06870.0031-0.4893-0.16020.05190.10870.0340.0781-0.12060.06240.02150.02730.1239-0.07940.1778-2.513314.691835.6545
23.2752-1.26510.4731.93560.19161.37820.11670.06260.1573-0.0628-0.06980.03380.1180.1366-0.04680.05420.0164-0.00690.0955-0.02620.032327.04467.653234.6479
33.23950.13890.18133.48530.55645.61920.0257-0.19750.5638-0.0680.05350.0699-0.34010.124-0.07920.04260.02240.00170.0679-0.06220.191120.908121.666532.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 51
2X-RAY DIFFRACTION2A52 - 124
3X-RAY DIFFRACTION3A125 - 177

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