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- PDB-4r9x: Crystal Structure of Putative Copper Homeostasis Protein CutC fro... -

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Basic information

Entry
Database: PDB / ID: 4r9x
TitleCrystal Structure of Putative Copper Homeostasis Protein CutC from Bacillus anthracis
ComponentsCopper homeostasis protein CutC
KeywordsMETAL TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / TIM barrel
Function / homology
Function and homology information


copper ion binding / cytoplasm
Similarity search - Function
Copper homeostasis (CutC) domain / Copper homeostasis protein CutC / Copper homeostasis (CutC) domain superfamily / CutC family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PF03932 family protein CutC / PF03932 family protein CutC
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8515 Å
AuthorsKim, Y. / Zhou, M. / Makowska-Grzyska, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2014
Title: Crystal Structure of Putative Copper Homeostasis Protein CutC from Bacillus anthracis
Authors: Kim, Y. / Zhou, M. / Makowska-Grzyska, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn_radiation
Item: _audit_author.name / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.3Nov 20, 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_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_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_asym_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_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: Copper homeostasis protein CutC
B: Copper homeostasis protein CutC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2568
Polymers51,8322
Non-polymers4256
Water2,954164
1
A: Copper homeostasis protein CutC
hetero molecules

B: Copper homeostasis protein CutC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2568
Polymers51,8322
Non-polymers4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.335, 58.335, 118.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Copper homeostasis protein CutC / Putative copper homeostasis protein CutC


Mass: 25915.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS2885, BA_3100, cutC, GBAA_3100 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q81NS5, UniProt: A0A6L8Q3J2*PLUS

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Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium acetate, 0.1 M sodium cacodylate pH 6.5, 40 %(w/v) PEG300, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 16, 2014 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 38473 / Num. obs: 38473 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 15.98 Å2 / Rsym value: 0.059 / Net I/σ(I): 24.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.31 / Num. unique all: 1990 / Rsym value: 0.642 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8515→28.329 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.8 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1890 5.04 %random
Rwork0.176 ---
all0.177 37508 --
obs0.177 37508 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8515→28.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 23 164 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093591
X-RAY DIFFRACTIONf_angle_d1.2184853
X-RAY DIFFRACTIONf_dihedral_angle_d16.431372
X-RAY DIFFRACTIONf_chiral_restr0.056586
X-RAY DIFFRACTIONf_plane_restr0.006626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8515-1.90150.22751280.20862376250479
1.9015-1.95730.21841510.20422686283791
1.9573-2.02040.25761370.20572828296595
2.0204-2.09250.23841630.20592792295594
2.0925-2.17620.20511380.19562795293394
2.1762-2.2750.22721420.19372761290394
2.275-2.39460.22361340.19042781291594
2.3946-2.54420.2481460.19672795294193
2.5442-2.740.28271540.20652730288493
2.74-3.01440.20331550.19672777293294
3.0144-3.44760.18031430.17422809295294
3.4476-4.33230.16461440.13192723286793
4.3323-17.32040.18111370.14192734287192
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)
11.9634-0.23310.80360.88080.20161.46130.1029-0.0576-0.1308-0.06290.02610.2252-0.0717-0.369-0.12360.09070.0271-0.00540.18240.01190.139116.007314.463431.5077
22.6370.32640.0033.8389-1.56397.11540.0615-0.22880.0043-0.0302-0.0632-0.0422-0.1286-0.05280.03920.1560.04160.01040.1584-0.01470.057526.808317.827144.101
31.12350.8147-0.80873.1394-0.33223.1789-0.0608-0.5833-0.24390.5246-0.23810.0978-0.0492-0.04630.22810.19330.03960.04720.33560.06460.168615.971714.247148.8752
41.93520.430.38960.58440.02731.03930.0153-0.5202-0.17480.22060.09130.3148-0.1113-0.6537-0.01260.17020.09190.0660.45140.06180.25569.678815.510748.5553
52.03250.7860.40911.197-0.44860.49440.0212-0.5332-0.10320.30980.07890.4681-0.0317-0.2969-0.04320.14650.07530.05630.59310.1250.4518-1.318113.571643.1078
60.86010.18910.14170.22410.14540.3752-0.0815-0.1895-0.02880.06120.07940.22740.0452-0.2360.0470.09420.0097-0.02450.47330.11620.4377-2.067812.116435.4157
71.5519-1.98880.35133.6953-1.52331.08370.19410.1635-0.4257-0.11820.08410.07270.5524-0.3834-0.27220.236-0.0285-0.11560.2535-0.02790.41510.20484.114422.884
82.9467-0.1725-3.66560.32990.19184.56070.10580.3240.0371-0.13860.00110.4103-0.3464-0.4605-0.09210.16020.0305-0.07330.50850.050.3396-1.513213.927223.7785
91.3192-0.53030.38421.2143-0.61371.35480.10080.0027-0.1962-0.0265-0.03480.00440.32810.3564-0.08070.14260.0617-0.02020.18460.00530.134.590554.769236.1999
102.25880.02152.07730.8019-0.36213.5338-0.00950.1504-0.001-0.0267-0.02320.0043-0.02060.33240.04580.09870.01590.01850.17730.00770.07952.390665.858624.283
111.67120.4984-0.23691.9290.67772.09350.08230.2178-0.2166-0.5653-0.08290.192-0.04420.1662-0.04290.31930.1579-0.0670.2494-0.10830.19823.462353.610818.0758
120.84630.25450.0441.1-0.33510.53450.09460.341-0.3552-0.34890.0315-0.18190.49180.5521-0.11520.3680.1946-0.03640.3698-0.09040.17858.599652.153717.345
131.7798-1.19390.0472.29280.03140.98780.17090.1154-0.2728-0.14550.01840.19840.28260.15030.11320.31280.2379-0.07460.2908-0.10080.27399.11745.898922.617
140.0045-0.0544-0.0270.89290.07420.28360.01190.2405-0.4438-0.15390.01-0.18370.25610.16830.0290.43850.2208-0.06750.3328-0.13520.481613.889440.149121.0637
150.9624-0.9155-0.44930.88020.48030.4907-0.1097-0.0633-0.32710.12230.07180.14660.15490.07230.10870.50020.2635-0.11840.2646-0.08980.562110.556633.712132.8502
161.5284-0.0949-0.27642.14130.26641.25720.0415-0.077-0.41010.2134-0.0261-0.020.31290.1269-0.02780.31420.099-0.08660.1880.00820.31255.967741.990337.4147
173.0688-1.0437-1.33841.9341-0.00862.4217-0.0816-0.4398-0.47510.38690.2087-0.04860.48840.2746-0.10410.43920.1043-0.08610.26620.0530.2717.52941.598544.3407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 183 )
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 202 )
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 213 )
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 225 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 66 )
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 100 )
12X-RAY DIFFRACTION12chain 'B' and (resid 101 through 137 )
13X-RAY DIFFRACTION13chain 'B' and (resid 138 through 154 )
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 176 )
15X-RAY DIFFRACTION15chain 'B' and (resid 177 through 191 )
16X-RAY DIFFRACTION16chain 'B' and (resid 192 through 206 )
17X-RAY DIFFRACTION17chain 'B' and (resid 207 through 225 )

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