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- PDB-3ded: C-terminal domain of Probable hemolysin from Chromobacterium violaceum -

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Basic information

Entry
Database: PDB / ID: 3ded
TitleC-terminal domain of Probable hemolysin from Chromobacterium violaceum
ComponentsProbable hemolysin
KeywordsMEMBRANE PROTEIN / hemolysin / Chromobacterium violaceum / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Membrane / Transmembrane
Function / homology
Function and homology information


flavin adenine dinucleotide binding / metal ion binding / plasma membrane
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. / Ion transporter-like, CBS domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / 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 / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of C-terminal domain of Probable hemolysin from Chromobacterium violaceum
Authors: Chang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJun 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: Probable hemolysin
B: Probable hemolysin
C: Probable hemolysin
D: Probable hemolysin
E: Probable hemolysin
F: Probable hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,76415
Polymers79,4046
Non-polymers3619
Water8,143452
1
A: Probable hemolysin
B: Probable hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5885
Polymers26,4682
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-39 kcal/mol
Surface area9290 Å2
MethodPISA, PQS
2
C: Probable hemolysin
D: Probable hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5885
Polymers26,4682
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-39 kcal/mol
Surface area9340 Å2
MethodPISA, PQS
3
E: Probable hemolysin
F: Probable hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5885
Polymers26,4682
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-37 kcal/mol
Surface area9280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.144, 55.312, 93.734
Angle α, β, γ (deg.)90.00, 94.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable hemolysin


Mass: 13233.957 Da / Num. of mol.: 6 / Fragment: residues 337-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_0231 / Plasmid: pET derivatives / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivatives / References: UniProt: Q7P1I2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M NaCacodylate pH 6.5, 0.2M Ca(OAC), 9%PEG4K., VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 26, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 37557 / Num. obs: 37093 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 21.34
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.84 / Num. unique all: 3664 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.251 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1847 5 %RANDOM
Rwork0.18578 ---
all0.18823 36956 --
obs0.18823 36956 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.544 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å2-1.07 Å2
2--1.22 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 9 452 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.945756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98423.291237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46115696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8981546
X-RAY DIFFRACTIONr_chiral_restr0.1060.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21981
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22862
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.230
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.52634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31324103
X-RAY DIFFRACTIONr_scbond_it2.17631840
X-RAY DIFFRACTIONr_scangle_it3.2764.51652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.137→2.192 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 123 -
Rwork0.178 2360 -
obs-2483 90.03 %
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)
16.5040.30810.76770.9317-0.42283.5944-0.09340.20740.00840.0487-0.03130.0776-0.1164-0.00080.1247-0.0823-0.0215-0.0053-0.0586-0.0171-0.072114.293318.3485-11.3738
23.66340.2255-0.34651.1637-0.69943.7895-0.0858-0.07410.27010.11850.11710.1607-0.443-0.2406-0.0313-0.0137-0.0023-0.0036-0.0511-0.00570.00098.822925.4974-4.0475
32.86520.6264-1.08813.35570.48412.8624-0.11530.3157-0.35750.0153-0.0047-0.12780.1219-0.12690.1199-0.0669-0.04930.0123-0.0347-0.0330.008225.052614.6266-21.3492
43.7065-1.82950.53511.6966-0.5543.8640.08530.198-0.3723-0.1044-0.1018-0.04680.38430.22060.0165-0.0095-0.0123-0.0019-0.023-0.0120.003235.334811.6765-25.7478
53.1026-0.70962.19637.34361.24774.8079-0.20890.03470.2534-0.1353-0.00210.2257-0.1274-0.27730.2109-0.0644-0.0194-0.0354-0.0524-0.0313-0.075938.21938.197542.2653
64.39941.36570.3945.59432.41486.86670.0367-0.25950.3476-0.1328-0.4110.7546-0.3843-1.1210.3743-0.04880.063-0.01610.1728-0.0799-0.019427.04146.363739.6907
72.69361.10810.31942.52540.99827.7232-0.11930.33750.0006-0.03840.0225-0.2098-0.0380.26780.0968-0.0696-0.02540.0025-0.0217-0.0046-0.075450.86618.452750.7953
85.166-0.05490.43554.83422.83117.77540.2208-0.0884-0.38980.03730.2837-0.65860.39141.3262-0.5044-0.05860.056-0.02330.1314-0.07150.030759.66554.092356.8027
92.4810.47420.35613.205-1.69762.8926-0.16240.02060.25060.03380.2337-0.0037-0.1393-0.2312-0.0713-0.08220.03660.0116-0.1185-0.0083-0.055519.71415.142315.6842
101.2649-0.9357-1.28365.5098-2.74914.4135-0.3074-0.25120.36960.8380.18-0.1133-0.61260.49360.12750.08230.0682-0.03960.007-0.00780.031419.184916.205618.5342
113.280.5009-1.30374.2271-0.75022.4398-0.04480.2764-0.1157-0.20920.20820.0181-0.04-0.1611-0.1634-0.0927-0.0043-0.0118-0.0709-0.018-0.09115.6214-9.765414.9431
121.79630.5764-0.85313.75660.85634.6519-0.18490.2046-0.1392-0.27430.17450.25060.2734-0.19730.0104-0.0303-0.0264-0.0216-0.0344-0.0025-0.01199.2318-18.89312.5195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A341 - 355
2X-RAY DIFFRACTION1A393 - 427
3X-RAY DIFFRACTION2A356 - 392
4X-RAY DIFFRACTION3B341 - 355
5X-RAY DIFFRACTION3B393 - 426
6X-RAY DIFFRACTION4B356 - 392
7X-RAY DIFFRACTION5C340 - 355
8X-RAY DIFFRACTION5C393 - 427
9X-RAY DIFFRACTION6C356 - 392
10X-RAY DIFFRACTION7D341 - 355
11X-RAY DIFFRACTION7D393 - 426
12X-RAY DIFFRACTION8D356 - 392
13X-RAY DIFFRACTION9E341 - 355
14X-RAY DIFFRACTION9E393 - 427
15X-RAY DIFFRACTION10E356 - 392
16X-RAY DIFFRACTION11F341 - 355
17X-RAY DIFFRACTION11F393 - 426
18X-RAY DIFFRACTION12F356 - 392

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