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- PDB-3gn6: Crystal structure of CT0912, ORFan protein from Chlorobium tepidu... -

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Entry
Database: PDB / ID: 3gn6
TitleCrystal structure of CT0912, ORFan protein from Chlorobium tepidum with a ferredoxin-like domain repeat (NP_661805.1) from CHLOROBIUM TEPIDUM TLS at 1.80 A resolution
ComponentsCT0912, ORFan protein with a ferredoxin-like domain repeat
Keywordsstructural genomics / unknown function / NP_661805.1 / CT0912 / ORFan protein from Chlorobium tepidum with a ferredoxin-like domain repeat / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologymetal ion binding / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of CT0912, ORFan protein from Chlorobium tepidum with a ferredoxin-like domain repeat (NP_661805.1) from CHLOROBIUM TEPIDUM TLS at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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_ref_seq_dif.details / _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: CT0912, ORFan protein with a ferredoxin-like domain repeat
B: CT0912, ORFan protein with a ferredoxin-like domain repeat
C: CT0912, ORFan protein with a ferredoxin-like domain repeat
D: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,73922
Polymers142,0834
Non-polymers1,65518
Water18,8261045
1
A: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7545
Polymers35,5211
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8355
Polymers35,5211
Non-polymers3154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0067
Polymers35,5211
Non-polymers4856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1445
Polymers35,5211
Non-polymers6234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: CT0912, ORFan protein with a ferredoxin-like domain repeat
B: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,58910
Polymers71,0422
Non-polymers5478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-52 kcal/mol
Surface area21500 Å2
MethodPISA
6
C: CT0912, ORFan protein with a ferredoxin-like domain repeat
D: CT0912, ORFan protein with a ferredoxin-like domain repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,14912
Polymers71,0422
Non-polymers1,10810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-52 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.268, 210.205, 57.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A21 - 320
2114B21 - 320
3114C21 - 320
4114D21 - 320

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CT0912, ORFan protein with a ferredoxin-like domain repeat


Mass: 35520.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Gene: CT0912, NP_661805.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8KDY2

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Non-polymers , 5 types, 1063 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2430M magnesium acetate, 13.6000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97949
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→46.829 Å / Num. obs: 137561 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.421 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.63
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.7491.74664312728199.5
1.86-1.940.5172.45370814638199.6
1.94-2.030.3683.35079913827199.7
2.03-2.130.2524.74713312805199.8
2.13-2.270.1916.15274014355199.9
2.27-2.440.1484908613341199.9
2.44-2.690.10310.85177714039199.9
2.69-3.070.079144977113586199.9
3.07-3.870.04720.45133214050199.8
3.87-23.4210.04424.14992714192197.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→46.829 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.354 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.85 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROLS, PEG FRAGMENTS (PEG AND 2PE) ARE PRESENT IN CYRO/CRYSTALLIZATION CONDITIONS. THE ASSIGNMENTS OF PEG FRAGMENTS AND GLYCEROLS ARE TENTATIVE DUE TO NOT WELL DEFINED DENSITY. 5. DISORDERED REGIONS: A33-34, A149-152,B149-152 AND D149-152. 6. MAGNESIUM IONS ARE ASSIGNED BASED COORDINATION, CRYSTALLIZATION CONDITIONS AND FLUORESCENCE SCAN WHICH INDICATES ABSENCE OF HEAVY METALS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 6913 5 %RANDOM
Rwork0.163 ---
obs0.164 137510 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.46 Å2 / Biso mean: 21.407 Å2 / Biso min: 4.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2---0.35 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9207 0 100 1045 10352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229854
X-RAY DIFFRACTIONr_bond_other_d0.0020.026628
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.95813494
X-RAY DIFFRACTIONr_angle_other_deg0.925316077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26451278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92422.597462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.062151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0391591
X-RAY DIFFRACTIONr_chiral_restr0.0930.21503
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022128
X-RAY DIFFRACTIONr_mcbond_it1.68736076
X-RAY DIFFRACTIONr_mcbond_other0.79832425
X-RAY DIFFRACTIONr_mcangle_it2.49959799
X-RAY DIFFRACTIONr_scbond_it4.18683778
X-RAY DIFFRACTIONr_scangle_it5.614113645
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3660 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.240.5
BMEDIUM POSITIONAL0.240.5
CMEDIUM POSITIONAL0.270.5
DMEDIUM POSITIONAL0.20.5
AMEDIUM THERMAL0.962
BMEDIUM THERMAL1.062
CMEDIUM THERMAL1.442
DMEDIUM THERMAL1.12
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 511 -
Rwork0.272 9530 -
all-10041 -
obs--99.4 %
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)
11.09080.2304-0.0460.4631-0.06170.4220.06990.1944-0.2703-0.0498-0.0205-0.0094-0.00120.0217-0.04940.04560.0437-0.05660.0732-0.09160.122116.3826132.60487.4242
20.94910.0127-0.06740.4352-0.00360.36520.1140.1756-0.1614-0.068-0.0451-0.0541-0.04090.089-0.06890.05090.0298-0.020.103-0.07810.080544.7865141.62967.8291
30.85450.18030.08720.6097-0.11260.28850.0069-0.09070.1238-0.0434-0.0123-0.0550.0179-0.06270.00540.0475-0.02660.0570.0332-0.03650.088946.7216190.780231.4555
40.77780.04740.07450.47490.0690.44990.0438-0.03430.1382-0.1039-0.030.1133-0.0296-0.0783-0.01370.0585-0.01870.01920.0369-0.03350.087418.2308184.193925.8644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 320
2X-RAY DIFFRACTION2B21 - 320
3X-RAY DIFFRACTION3C20 - 320
4X-RAY DIFFRACTION4D21 - 320

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