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- PDB-2iz7: structure of Moco Carrier Protein from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 2iz7
Titlestructure of Moco Carrier Protein from Chlamydomonas reinhardtii
ComponentsMOCO CARRIER PROTEIN
KeywordsMETAL TRANSPORT / MOLYBDENUM COFACTOR
Function / homologySLOG cluster4 / SLOG cluster4 family / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Molybdenum cofactor carrier protein
Function and homology information
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsFischer, K. / Llamas, A. / Tejada-Jimenez, M. / Schrader, N. / Kuper, J. / Mendel, R.R. / Fernandez, E. / Schwarz, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Function and Structure of the Molybdenum Cofactor Carrier Protein from Chlamydomonas Reinhardtii.
Authors: Fischer, K. / Llamas, A. / Tejada-Jimenez, M. / Schrader, N. / Kuper, J. / Ataya, F.S. / Galvan, A. / Mendel, R.R. / Fernandez, E. / Schwarz, G.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MOCO CARRIER PROTEIN
B: MOCO CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,7772
Polymers35,7772
Non-polymers00
Water4,179232
1
A: MOCO CARRIER PROTEIN
B: MOCO CARRIER PROTEIN

A: MOCO CARRIER PROTEIN
B: MOCO CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)71,5554
Polymers71,5554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7360 Å2
ΔGint-56.2 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.558, 124.548, 74.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MOCO CARRIER PROTEIN


Mass: 17888.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Plasmid: PQE80-CRMCP1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: Q8RV61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 47.9 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→62.3 Å / Num. obs: 16385 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.7
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IZ6

2iz6


Resolution: 2.32→62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.751 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS ARE PARTIALLY TRACED WITH ALANINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 701 5 %RANDOM
Rwork0.181 ---
obs0.185 13324 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---2.98 Å20 Å2
3---2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.32→62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 232 2487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222291
X-RAY DIFFRACTIONr_bond_other_d0.0010.022260
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9873108
X-RAY DIFFRACTIONr_angle_other_deg0.94635247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.755321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.51525.87363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47715381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.433157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.2490.2641
X-RAY DIFFRACTIONr_nbd_other0.1930.22464
X-RAY DIFFRACTIONr_nbtor_refined0.170.21126
X-RAY DIFFRACTIONr_nbtor_other0.0930.21479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2213
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2391.51986
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46722519
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2353759
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.444.5589
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 56
Rwork0.193 962
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)
13.1984-1.1943-0.95833.4905-0.45553.8236-0.0424-0.39390.05120.38610.2363-0.2730.08020.3354-0.1939-0.0818-0.0664-0.0458-0.15-0.0161-0.064423.257317.108227.283
21.4647-1.4376-0.59942.50660.23091.25160.0605-0.06180.2131-0.01040.0023-0.0535-0.0944-0.106-0.0628-0.0674-0.0359-0.0226-0.06650.0158-0.012717.648224.41120.0522
33.58881.06690.61015.08320.70544.9439-0.14840.3556-0.0194-0.28560.2556-0.1893-0.24620.144-0.1072-0.0750.0507-0.0306-0.1893-0.0043-0.120420.685953.612714.1665
42.22681.1608-0.12792.2334-0.38170.9137-0.0364-0.0184-0.13340.11580.0391-0.0731-0.06820.0181-0.00260.01950.02860.0015-0.03320.0021-0.033117.921646.266422.6365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 73
2X-RAY DIFFRACTION2A76 - 167
3X-RAY DIFFRACTION3B4 - 73
4X-RAY DIFFRACTION4B76 - 166

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