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- PDB-7me6: Structure of the apo form of YcnI -

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Basic information

Entry
Database: PDB / ID: 7me6
TitleStructure of the apo form of YcnI
ComponentsUncharacterized protein YcnI
KeywordsMETAL BINDING PROTEIN / cupredoxin / Cu-binding
Function / homologyYcnI-like / YcnI-like superfamily / Domain of unkown function (DUF1775) / plasma membrane / MALONATE ION / Uncharacterized protein YcnI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsDamle, M. / Fisher, O.S.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The YcnI protein from Bacillus subtilis contains a copper-binding domain.
Authors: Damle, M.S. / Singh, A.N. / Peters, S.C. / Szalai, V.A. / Fisher, O.S.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YcnI
B: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0924
Polymers28,8882
Non-polymers2042
Water4,540252
1
A: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5462
Polymers14,4441
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5462
Polymers14,4441
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.425, 90.425, 208.471
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-433-

HOH

31A-437-

HOH

41A-438-

HOH

51A-440-

HOH

61B-395-

HOH

71B-411-

HOH

81B-412-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 154)
21(chain B and resid 28 through 154)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 28 - 154 / Label seq-ID: 2 - 128

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 28 through 154)AA
2(chain B and resid 28 through 154)BB

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Components

#1: Protein Uncharacterized protein YcnI


Mass: 14443.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ycnI, BSU03940 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P94431
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid, 2.394 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→39.1 Å / Num. obs: 59466 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.997 / Rrim(I) all: 0.138 / Net I/σ(I): 12.06
Reflection shellResolution: 2.05→2.11 Å / Mean I/σ(I) obs: 1.77 / Num. unique obs: 4302 / CC1/2: 0.516

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cu YcnI (to be deposited)

Resolution: 2.053→38.482 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2000 6.19 %
Rwork0.1963 30328 -
obs0.1978 32328 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.91 Å2 / Biso mean: 48.1747 Å2 / Biso min: 22.27 Å2
Refinement stepCycle: final / Resolution: 2.053→38.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 14 252 2299
Biso mean--71.61 50.36 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072112
X-RAY DIFFRACTIONf_angle_d0.982878
X-RAY DIFFRACTIONf_chiral_restr0.062304
X-RAY DIFFRACTIONf_plane_restr0.007375
X-RAY DIFFRACTIONf_dihedral_angle_d11.2711244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1198X-RAY DIFFRACTION7.313TORSIONAL
12B1198X-RAY DIFFRACTION7.313TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.053-2.10440.29341360.2634206198
2.1044-2.16130.28211390.23222109100
2.1613-2.22490.25811400.22132124100
2.2249-2.29670.28541410.22012128100
2.2967-2.37870.24811400.21212137100
2.3787-2.4740.24651390.20592111100
2.474-2.58650.22021430.20892153100
2.5865-2.72290.23691410.21422143100
2.7229-2.89340.22831410.22432155100
2.8934-3.11670.25731440.21542175100
3.1167-3.43020.23041430.19272170100
3.4302-3.92610.22291460.18112213100
3.9261-4.94490.18121480.16322236100
4.9449-38.4820.19531590.19512413100
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)
19.0398-3.0182-5.36169.01684.71924.5005-0.24610.5036-0.4378-0.47610.1221-0.08370.0987-0.26160.08630.3278-0.0481-0.00950.35460.03820.2254-3.801-10.8159.8391
25.7652-0.7004-1.0713.76280.38533.9433-0.0657-0.0257-0.45380.31990.05860.07230.5691-0.16490.01620.3022-0.0541-0.00550.24290.06370.2611-5.3852-14.113621.4204
35.31360.7136-0.16512.1432.69285.1408-0.23191.7745-1.2557-0.28960.2201-0.05181.7162-0.00660.0120.7563-0.0581-0.01690.6281-0.1730.4295-2.2449-20.37543.9552
48.4894-0.2175-4.66143.33120.90596.4274-0.17610.5629-0.377-0.36340.16260.5180.1213-0.4310.10380.3786-0.143-0.01760.32610.02950.4147-14.9324-16.607313.9473
58.1099-0.05552.14919.5054-4.65113.68290.3472-0.2497-0.29110.5033-0.5751-0.8988-0.10470.23750.18150.3798-0.1019-0.00240.32220.02450.3413-34.5032-22.489742.184
67.85021.35660.30887.5569-2.58227.13620.05281.13390.8391-0.1617-0.1540.0331-0.3367-0.00310.06780.3459-0.04740.12030.28840.10160.3846-34.1493-10.580328.6411
76.0766.43855.74016.79056.10255.64940.0994-0.03240.11050.214-0.3806-1.5819-0.01970.87060.23240.3643-0.0413-0.08670.4350.02110.6876-25.4877-27.183637.8369
83.79984.14263.99116.0742.36988.7253-0.69910.5854-0.2733-0.85070.6565-0.628-0.15130.52570.22360.4528-0.0390.12650.3843-0.0120.322-31.849-24.744426.3384
93.4056-4.70451.01277.9876-1.69177.54110.06671.37961.1908-0.3372-0.4358-0.95140.10270.91640.23710.4155-0.10130.11050.40930.06460.5666-30.2005-18.284727.8493
105.11432.18350.12816.2248-0.7584.36810.32020.1390.29230.3323-0.2889-0.6234-0.11730.55430.01290.2894-0.05880.06670.33130.00630.3912-30.1479-17.02736.5025
117.7592-1.0135-0.77985.8726-4.31548.17660.4629-0.76230.43981.9233-0.1337-0.3206-1.0435-0.2577-0.32910.6462-0.24120.02240.477-0.04130.3751-28.4822-12.542546.3401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 48 )A27 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 113 )A49 - 113
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 123 )A114 - 123
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 154 )A124 - 154
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 48 )B27 - 48
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 61 )B49 - 61
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 71 )B62 - 71
8X-RAY DIFFRACTION8chain 'B' and (resid 72 through 83 )B72 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 104 )B84 - 104
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 137 )B105 - 137
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 154 )B138 - 154

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