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- PDB-4clv: Crystal Structure of dodecylphosphocholine-solubilized NccX from ... -

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Basic information

Entry
Database: PDB / ID: 4clv
TitleCrystal Structure of dodecylphosphocholine-solubilized NccX from Cupriavidus metallidurans 31A
ComponentsNICKEL-COBALT-CADMIUM RESISTANCE PROTEIN NCCX
KeywordsMETAL BINDING PROTEIN / MEMBRANE PROTEIN / NICKEL-COBALT RESISTANCE
Function / homologyHeavy-metal resistance protein / Heavy-metal resistance / response to cadmium ion / PHOSPHOCHOLINE / PHOSPHATE ION / Nickel-cobalt-cadmium resistance protein NccX
Function and homology information
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.12 Å
AuthorsLegrand, P. / Girard, E. / Petit-Hartlein, I. / Maillard, A.P. / Coves, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The X-Ray Structure of Nccx from Cupriavidus Metallidurans 31A Illustrates Potential Dangers of Detergent Solubilization When Generating and Interpreting Crystal Structures of Membrane Proteins.
Authors: Ziani, W. / Maillard, A.P. / Petit-Hartlein, I. / Garnier, N. / Crouzy, S. / Girard, E. / Coves, J.
History
DepositionJan 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Mar 25, 2015Group: Atomic model
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: NICKEL-COBALT-CADMIUM RESISTANCE PROTEIN NCCX
B: NICKEL-COBALT-CADMIUM RESISTANCE PROTEIN NCCX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,82618
Polymers33,4242
Non-polymers1,40216
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-16 kcal/mol
Surface area21510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)53.800, 53.800, 300.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.962, -0.092, -0.256), (0.009, -0.952, 0.307), (-0.272, 0.293, 0.917)
Vector: -5.392, -10.625, 0.57)

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Components

#1: Protein NICKEL-COBALT-CADMIUM RESISTANCE PROTEIN NCCX


Mass: 16712.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: 31A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q44582
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P

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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: 3.25 Å3/Da / Density % sol: 58.5 % / Description: NONE
Crystal growpH: 4.5
Details: 14 % PEG4000 0.1 M NA-ACETATE PH 4.5 0.1 M ZN-ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28202
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28202 Å / Relative weight: 1
ReflectionResolution: 3.12→47.38 Å / Num. obs: 8629 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 23.6 % / Biso Wilson estimate: 132.09 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.5
Reflection shellResolution: 3.12→3.34 Å / Redundancy: 25.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.12→25 Å / Cor.coef. Fo:Fc: 0.9374 / Cor.coef. Fo:Fc free: 0.9265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.432
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 430 5 %RANDOM
Rwork0.251 ---
obs0.2517 8604 99.98 %-
Displacement parametersBiso mean: 164.48 Å2
Baniso -1Baniso -2Baniso -3
1--22.0805 Å20 Å20 Å2
2---22.0805 Å20 Å2
3---44.161 Å2
Refine analyzeLuzzati coordinate error obs: 1.315 Å
Refinement stepCycle: LAST / Resolution: 3.12→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 52 0 2290
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092308HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043128HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d834SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes334HARMONIC5
X-RAY DIFFRACTIONt_it2308HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion20.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2657SEMIHARMONIC4
LS refinement shellResolution: 3.12→3.49 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2954 118 4.99 %
Rwork0.2815 2247 -
all0.2822 2365 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: -6.1024 Å / Origin y: -1.068 Å / Origin z: 26.7969 Å
111213212223313233
T0.304 Å2-0.0085 Å20.0024 Å2--0.304 Å2-0.1014 Å2---0.0104 Å2
L2.4672 °2-0.2458 °2-0.0397 °2-4.2495 °20.5229 °2--6.7292 °2
S0.3445 Å °0.1511 Å °0.1335 Å °0.2902 Å °-0.1447 Å °-0.062 Å °-0.5442 Å °0.4455 Å °-0.1998 Å °
Refinement TLS groupSelection details: CHAINS A AND B

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