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- PDB-2iz6: Structure of the Chlamydomonas rheinhardtii Moco Carrier Protein -

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Basic information

Entry
Database: PDB / ID: 2iz6
TitleStructure of the Chlamydomonas rheinhardtii Moco Carrier Protein
ComponentsMOLYBDENUM COFACTOR 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 26, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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: MOLYBDENUM COFACTOR CARRIER PROTEIN
B: MOLYBDENUM COFACTOR CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,7772
Polymers35,7772
Non-polymers00
Water4,414245
1
A: MOLYBDENUM COFACTOR CARRIER PROTEIN
B: MOLYBDENUM COFACTOR CARRIER PROTEIN

A: MOLYBDENUM COFACTOR CARRIER PROTEIN
B: MOLYBDENUM COFACTOR 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 area7190 Å2
ΔGint-59.5 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.079, 126.009, 75.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2081-

HOH

21B-2069-

HOH

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Components

#1: Protein MOLYBDENUM COFACTOR 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.: 245 / 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: 2.5 Å3/Da / Density % sol: 49.5 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.005
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 38713 / % possible obs: 88.2 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 55.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IZ5

2iz5


Resolution: 1.6→75.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.71 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES A1-A2,A71-A75,A167-A173, B1-B3,B70-B76,B167-B173. DISORDERED REGIONS ARE PARTIALLY TRACED WITH ALANINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2080 5 %RANDOM
Rwork0.184 ---
obs0.186 39120 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---1.65 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.6→75.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 245 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222259
X-RAY DIFFRACTIONr_bond_other_d0.0010.022230
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9873071
X-RAY DIFFRACTIONr_angle_other_deg0.92735187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82826.1963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08915383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511156
X-RAY DIFFRACTIONr_chiral_restr0.110.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
X-RAY DIFFRACTIONr_nbd_refined0.2320.2473
X-RAY DIFFRACTIONr_nbd_other0.180.22212
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21139
X-RAY DIFFRACTIONr_nbtor_other0.0920.21481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7171.51968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95922479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3433751
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7024.5586
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 141
Rwork0.247 2977
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)
11.6955-0.1968-0.92551.79540.12231.83710.0111-0.11870.02160.14210.0518-0.19090.07280.0249-0.06290.0201-0.02320.0021-0.0767-0.0065-0.043122.54816.38527.39
20.6425-0.2316-0.36892.274-0.17330.39010.05770.06870.074-0.0270.006-0.0258-0.0056-0.1032-0.0638-0.012-0.00790.0101-0.06350.0161-0.050817.87924.620.522
30.95390.3593-0.10863.88990.2891.4772-0.05880.09630.1071-0.090.08870.0635-0.1537-0.02-0.02990.01740.0216-0.032-0.08170.0097-0.05520.07254.74314.557
41.60630.83020.07492.4369-0.390.47150.0205-0.087-0.03840.2403-0.02630.0499-0.0929-0.07010.00570.00850.02990.0062-0.0760.0109-0.071917.97246.53822.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 69
2X-RAY DIFFRACTION2A76 - 166
3X-RAY DIFFRACTION3B4 - 69
4X-RAY DIFFRACTION4B77 - 166

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