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- PDB-2pls: Structural Genomics, the crystal structure of the CorC/HlyC trans... -

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Basic information

Entry
Database: PDB / ID: 2pls
TitleStructural Genomics, the crystal structure of the CorC/HlyC transporter associated domain of a CBS domain protein from Chlorobium tepidum TLS
ComponentsCBS domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86064.2 / CorC/HlyC transporter associated domain / CBS domain protein / Chlorobium tepidum TLS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / CBS domain protein
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsTan, K. / Volkart, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the CorC/HlyC transporter associated domain of a CBS domain protein from Chlorobium tepidum TLS.
Authors: Tan, K. / Volkart, L. / Clancy, S. / Joachimiak, A.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Remark 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ... BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 CHAINS. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. THE ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBS domain protein
B: CBS domain protein
C: CBS domain protein
D: CBS domain protein
E: CBS domain protein
F: CBS domain protein
G: CBS domain protein
H: CBS domain protein
I: CBS domain protein
J: CBS domain protein
K: CBS domain protein
L: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,82841
Polymers119,36312
Non-polymers1,46529
Water10,070559
1
A: CBS domain protein
B: CBS domain protein
C: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,36412
Polymers29,8413
Non-polymers5249
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: CBS domain protein
E: CBS domain protein
F: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,31511
Polymers29,8413
Non-polymers4748
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: CBS domain protein
H: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9675
Polymers19,8942
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: CBS domain protein
J: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1839
Polymers19,8942
Non-polymers2897
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: CBS domain protein
hetero molecules

K: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0124
Polymers19,8942
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
6
L: CBS domain protein
hetero molecules

L: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9864
Polymers19,8942
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)108.243, 108.493, 106.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11K-927-

HOH

21K-942-

HOH

DetailsExperimentally unknown. However, the Chains, A,B and C possibly form a trimer. The Chains, D,E and F possiblly form a similar trimer. The Chains, G and H possiblly form a dimer. The Chains, I and J possiblly form a similar dimer. The Chain K possiblly forms a similar dimer with its symmetry-related molecule by an operator of (-x+1,-y,z). The Chain L possiblly forms a similar dimer with its symmetry-related molecule by an operator of (-x+1,-y,z).

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
CBS domain protein /


Mass: 9946.923 Da / Num. of mol.: 12 / Fragment: CorC/HlyC transporter associated domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS, DSM 12025 / Gene: CT0541 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KEZ1

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Non-polymers , 5 types, 588 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl, 0.1M Tris-HCl, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921, 0.97938
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979381
ReflectionResolution: 2.15→48.51 Å / Num. all: 68297 / Num. obs: 68297 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 30.4
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6599 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→48.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.966 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.214 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23203 3453 5.1 %RANDOM
Rwork0.17582 ---
all0.1787 64784 --
obs0.1787 64784 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8218 0 92 559 8869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.97311507
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31151035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25824.418378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09151573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0941563
X-RAY DIFFRACTIONr_chiral_restr0.1250.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026233
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23797
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25673
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2545
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.55326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45728260
X-RAY DIFFRACTIONr_scbond_it2.30933784
X-RAY DIFFRACTIONr_scangle_it3.5384.53237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 212 -
Rwork0.209 4571 -
obs-4783 94.92 %
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)
13.65921.18480.14646.4195-2.73495.51030.1385-0.19980.35951.0867-0.6001-0.4647-0.9150.37950.4616-0.0785-0.1846-0.1682-0.16280.04510.041684.85340.56358.119
24.52460.74990.43364.1745-1.07843.4767-0.0344-0.67480.02510.5891-0.133-0.1904-0.169-0.02340.1674-0.1825-0.014-0.08290.02110.0921-0.133778.64219.55768.417
33.73040.2519-0.0643.3666-1.31241.8109-0.05150.10440.3531-0.04660.09410.1994-0.0203-0.0644-0.0426-0.1944-0.0238-0.0295-0.12190.0488-0.060267.33827.29948.439
42.27440.614-0.03311.6262-0.46642.88270.0271-0.27660.12560.0299-0.0748-0.1051-0.10110.18880.0477-0.1202-0.03860.068-0.1321-0.0011-0.088183.48929.97120.076
53.19250.675-0.59023.48570.46813.1412-0.1053-0.021-0.2971-0.3599-0.0005-0.51120.03310.34290.1058-0.0819-0.02890.1887-0.14490.0642-0.010996.5723.555100.49
61.44360.1569-0.95432.9352-0.14413.2277-0.03480.0392-0.0802-0.0707-0.03830.05580.3491-0.23480.0731-0.0504-0.08340.0713-0.1328-0.0099-0.139975.82611.817105.768
71.6133-0.8566-1.27986.69760.03572.91510.0514-0.00480.06140.4336-0.1041-0.1784-0.08670.30970.0526-0.1220.01230.0668-0.16810.0385-0.096292.871-4.61593.305
85.5212-1.61493.03875.3957-3.39497.55820.32560.9663-0.2237-0.4815-0.561-0.21790.64741.1320.2354-0.25410.1651-0.00030.13160.0287-0.175695.7022.04769.651
93.4053-0.1449-0.20275.7767-0.08675.33320.06240.0617-0.13560.0333-0.0130.8836-0.1225-0.3686-0.0494-0.2277-0.02480.0415-0.1939-0.01420.043799.29641.29483.527
102.896-1.2387-0.19492.6303-0.45734.4051-0.0985-0.0863-0.00750.4010.0537-0.04-0.30460.27410.0448-0.10650.02780.0166-0.15680.0672-0.1293123.39541.03977.95
116.36910.6585-0.86754.6806-1.42943.36870.1193-0.30270.04610.3215-0.1368-0.0234-0.07820.19390.0176-0.22710.01960.051-0.13910.0703-0.110750.58212.33862.958
128.82710.73050.28764.44171.02023.77690.06470.09160.7683-0.4336-0.09660.2838-0.2408-0.30330.0319-0.092-0.04670.0009-0.12180.0115-0.203657.50412.36389.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA343 - 4281 - 86
2X-RAY DIFFRACTION2BB343 - 4281 - 86
3X-RAY DIFFRACTION3CC343 - 4281 - 86
4X-RAY DIFFRACTION4DD343 - 4271 - 85
5X-RAY DIFFRACTION5EE343 - 4271 - 85
6X-RAY DIFFRACTION6FF343 - 4271 - 85
7X-RAY DIFFRACTION7GG343 - 4271 - 85
8X-RAY DIFFRACTION8HH344 - 4282 - 86
9X-RAY DIFFRACTION9II343 - 4281 - 86
10X-RAY DIFFRACTION10JJ343 - 4281 - 86
11X-RAY DIFFRACTION11KK343 - 4281 - 86
12X-RAY DIFFRACTION12LL343 - 4281 - 86

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