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- PDB-2p3h: Crystal structure of the CorC_HlyC domain of a putative Corynebac... -

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Basic information

Entry
Database: PDB / ID: 2p3h
TitleCrystal structure of the CorC_HlyC domain of a putative Corynebacterium glutamicum hemolysin
ComponentsUncharacterized CBS domain-containing protein
KeywordsTRANSPORT PROTEIN / structural genomics / CorC_HlyC / pfam03471 / Putative transport protein / Transporter associated domain / Corynebacterium glutamicum / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / membrane => GO:0016020
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
BROMIDE ION / Uncharacterized CBS domain-containing proteins
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Volkart, L. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the CorC_HlyC domain of a putative Corynebacterium glutamicum hemolysin.
Authors: Cuff, M.E. / Volkart, L. / Gu, M. / Joachimiak, A.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 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
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN. THE CRYSTALLIZED DOMAIN IS PART OF MUCH LARGER PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,19313
Polymers11,2881
Non-polymers90512
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.200, 51.214, 101.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

Detailsunknown, maybe monomer

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Components

#1: Protein Uncharacterized CBS domain-containing protein / Membrane protein containing CBS domain / putative hemolysin


Mass: 11287.524 Da / Num. of mol.: 1 / Fragment: CorC_HlyC domain: residues 356-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: TlyC, Cgl1194, cg1349 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NR63
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2M (NH4)2SO4, 0.1M Cacodylate pH 6.5, 0.2M NaCl, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.91946 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 23, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91946 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 13.3 / Number: 104059 / Rmerge(I) obs: 0.064 / Χ2: 2.18 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 13454 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.225096.910.0547.2387.2
3.354.2210010.0473.5968
2.923.3599.910.05438.4
2.662.9299.910.0682.6458.6
2.472.6610010.0751.9958.7
2.322.4710010.0891.7078.8
2.22.3210010.11.4988.8
2.112.210010.1091.2348.9
2.032.1110010.1361.1988.9
1.962.0310010.1771.0468.8
1.91.9699.610.2191.0498
1.841.998.110.3051.0155.6
1.791.8490.910.3731.0264.6
1.751.7977.710.3931.0163.7
ReflectionResolution: 1.75→50 Å / Num. all: 13454 / Num. obs: 13454 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.064 / Χ2: 2.179 / Net I/σ(I): 13.3
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.393 / Num. unique all: 749 / Χ2: 1.016 / % possible all: 77.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.75 Å / D res low: 50 Å / FOM : 0.257 / FOM acentric: 0.29 / FOM centric: 0 / Reflection: 13421 / Reflection acentric: 11856 / Reflection centric: 1565
Phasing MAD setR cullis acentric: 1.73 / R cullis centric: 1 / Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 11856 / Reflection centric: 1565
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
11.25-501.690.40.22627
6.34-11.251.380.30.218271
4.41-6.341.50.30.2478129
3.38-4.411.170.20.2898185
2.74-3.381.50.10.11469233
2.31-2.742.090.102170275
1.99-2.312.74003002318
1.75-1.9910.33003631327
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Br36.089740.720.2230.0620
2Br42.213530.5620.4150.1840
3Br42.953280.7010.1980.2330
4Br32.264480.630.3030.3160
5Br54.300460.5270.0420.1430
6Br51.054230.5380.340.3050
7Br26.592510.6610.2540.2660
8Br67.931820.873-0.0260.0520
9Br45.966010.7660.2570.0880
10Br34.9580.7480.2790.2170
11Br31.670.5270.0380.2460
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.25-500.2220.4520532627
6.34-11.250.3570.497025318271
4.41-6.340.3960.5030607478129
3.38-4.410.4060.4901083898185
2.74-3.380.4210.488017021469233
2.31-2.740.3430.386024452170275
1.99-2.310.2250.249033203002318
1.75-1.990.0910.099039583631327
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13421
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.37-10061.90.759506
4.25-5.3758.70.897503
3.7-4.2560.20.874511
3.36-3.760.80.862505
3.12-3.3661.80.866503
2.93-3.1265.70.82509
2.78-2.9361.10.834507
2.66-2.7864.20.822501
2.55-2.6660.80.846506
2.46-2.55620.841512
2.38-2.4666.30.837516
2.31-2.38620.853524
2.25-2.3165.70.814522
2.18-2.2568.70.797578
2.13-2.1865.90.826532
2.08-2.1366.40.844609
2.03-2.0869.90.825596
1.98-2.0371.50.814606
1.94-1.9873.60.794633
1.9-1.9475.10.835611
1.87-1.984.10.81651
1.83-1.8782.40.748625
1.8-1.8379.50.71605
1.75-1.881.90.691750

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.865 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 625 5 %RANDOM
Rwork0.193 ---
all0.195 12619 --
obs0.195 12619 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--1.87 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 21 172 969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022866
X-RAY DIFFRACTIONr_angle_refined_deg1.4282.0131191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66925.90944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18315148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.255155
X-RAY DIFFRACTIONr_chiral_restr0.1030.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02671
X-RAY DIFFRACTIONr_nbd_refined0.2190.2419
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.220
X-RAY DIFFRACTIONr_mcbond_it0.8661.5542
X-RAY DIFFRACTIONr_mcangle_it1.3312868
X-RAY DIFFRACTIONr_scbond_it2.1413363
X-RAY DIFFRACTIONr_scangle_it3.4784.5318
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 39 -
Rwork0.239 802 -
obs-841 91.81 %
Refinement TLS params.Method: refined / Origin x: 0.0277 Å / Origin y: -13.659 Å / Origin z: 8.0446 Å
111213212223313233
T-0.1423 Å20.0125 Å20.0165 Å2--0.2123 Å20.0049 Å2---0.1724 Å2
L3.1511 °2-0.1067 °20.0319 °2-1.0229 °20.5391 °2--3.2127 °2
S0.1731 Å °-0.1023 Å °-0.0316 Å °-0.0828 Å °-0.0732 Å °0.1127 Å °-0.1198 Å °-0.0618 Å °-0.0999 Å °
Refinement TLS groupSelection: ALL

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