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- PDB-2vql: Crystal structure of PorB from Corynebacterium glutamicum (crysta... -

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Basic information

Entry
Database: PDB / ID: 2vql
TitleCrystal structure of PorB from Corynebacterium glutamicum (crystal form III)
ComponentsUNCHARACTERIZED PROTEIN CGL0972
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT
Function / homology
Function and homology information


Alpha-helical porin B/porin C / Porin PorB/PorC / Alpha-helical PorB/PorC / Alpha helical Porin B / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / PorB
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsZiegler, K. / Benz, R. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A Putative Alpha-Helical Porin from Corynebacterium Glutamicum.
Authors: Ziegler, K. / Benz, R. / Schulz, G.E.
History
DepositionMar 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _citation.page_last / _database_2.pdbx_DOI ..._citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNCHARACTERIZED PROTEIN CGL0972
B: UNCHARACTERIZED PROTEIN CGL0972
C: UNCHARACTERIZED PROTEIN CGL0972
D: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,90720
Polymers42,5744
Non-polymers1,33316
Water00
1
A: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1797
Polymers10,6441
Non-polymers5366
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1797
Polymers10,6441
Non-polymers5366
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7743
Polymers10,6441
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7743
Polymers10,6441
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.392, 78.392, 191.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
UNCHARACTERIZED PROTEIN CGL0972 / PORB / ANION-SPECIFIC PORIN / ANION-SPECIFIC PORIN PRECURSOR


Mass: 10643.550 Da / Num. of mol.: 4 / Fragment: RESIDUES 28-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NRS3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.16→60.75 Å / Num. obs: 10828 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 8.4 % / Rsym value: 0.06 / Net I/σ(I): 23.9
Reflection shellRedundancy: 8.8 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.36 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16→60.75 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.87 / SU B: 39.254 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R: 1.225 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 542 5 %RANDOM
Rwork0.281 ---
obs0.282 10285 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 3.16→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 32 0 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9111.9343116
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34826.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8315343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.594158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21047
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21584
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.272
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_it01.51446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it022253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it03846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it04.5863
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: 3.16→3.24 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.395 40
Rwork0.316 749
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)
13.87080.9688-4.57665.8009-1.322114.28070.08860.8017-0.24760.4091-0.2803-0.2866-0.2092-0.40070.1917-0.5491-0.0902-0.0068-0.1232-0.0767-0.3023-20.990316.9964-18.7186
24.2511-3.39853.03169.8985-6.39948.08210.1040.2159-0.1365-0.3678-0.00080.07830.4133-0.4321-0.1032-0.5541-0.07920.09670.0679-0.12-0.319-37.97878.4539-21.6758
34.9431.167-0.72243.6763-2.381518.3917-0.12470.22080.06560.60540.24590.242-1.068-0.0451-0.12120.2784-0.0694-0.1319-0.5251-0.0178-0.1738-21.607120.40398.6464
412.3819-2.6337-3.21518.94891.493410.86660.2402-0.3489-0.43720.5877-0.59491.1669-0.3821-0.76580.3548-0.4402-0.10920.04610.1077-0.0137-0.0819-39.9212-13.9882-10.5649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 88
2X-RAY DIFFRACTION2B16 - 88
3X-RAY DIFFRACTION3C13 - 88
4X-RAY DIFFRACTION4D17 - 87

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