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- PDB-1nvj: Deletion Mutant (Delta 141) of Molybdopterin Synthase -

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Basic information

Entry
Database: PDB / ID: 1nvj
TitleDeletion Mutant (Delta 141) of Molybdopterin Synthase
ComponentsMolybdopterin converting factor subunit 2
KeywordsTRANSFERASE / Deletion Mutant / Molybdenum cofactor biosynthesis
Function / homology
Function and homology information


molybdopterin synthase complex / molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Molybdopterin synthase catalytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRudolph, M.J. / Wuebbens, M.M. / Turque, O. / Rajagopalan, K.V. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural Studies of Molybdopterin Synthase Provide Insights into its Catalytic Mechanism
Authors: Rudolph, M.J. / Wuebbens, M.M. / Turque, O. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionFeb 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Molybdopterin converting factor subunit 2
B: Molybdopterin converting factor subunit 2
C: Molybdopterin converting factor subunit 2
D: Molybdopterin converting factor subunit 2
E: Molybdopterin converting factor subunit 2
F: Molybdopterin converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,90924
Polymers94,8046
Non-polymers1,10518
Water5,945330
1
A: Molybdopterin converting factor subunit 2
B: Molybdopterin converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0859
Polymers31,6012
Non-polymers4837
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-15 kcal/mol
Surface area11280 Å2
MethodPISA
2
C: Molybdopterin converting factor subunit 2
D: Molybdopterin converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,10810
Polymers31,6012
Non-polymers5068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-14 kcal/mol
Surface area12500 Å2
MethodPISA
3
E: Molybdopterin converting factor subunit 2
F: Molybdopterin converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7175
Polymers31,6012
Non-polymers1153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.128, 127.832, 138.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe Biological Assembly is a Dimer. There are Three Dimers in the Asymmetric Unit.

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Components

#1: Protein
Molybdopterin converting factor subunit 2 / MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis ...MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin converting factor large subunit


Mass: 15800.741 Da / Num. of mol.: 6 / Fragment: residues 0-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MOAE OR CHLA5 OR B0785 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30749
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.6 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 10% Isopropanol and 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1600 mMsodium formate1reservoir
215 %PEG40001reservoir
310 %isopropanol1reservoir
4100 mMTris1reservoirpH7.5
520 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2002 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→47.14 Å / Num. all: 47232 / Num. obs: 47232 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 17.9
Reflection shellHighest resolution: 2.15 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.367 / % possible all: 73.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 167567
Reflection shell
*PLUS
% possible obs: 73.1 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FM0

1fm0


Resolution: 2.15→47.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.234 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22704 2394 5.1 %RANDOM
Rwork0.17654 ---
all0.17901 47231 --
obs0.17901 44837 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5903 0 70 330 6303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216128
X-RAY DIFFRACTIONr_bond_other_d0.0020.025531
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9328303
X-RAY DIFFRACTIONr_angle_other_deg0.83312798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565729
X-RAY DIFFRACTIONr_chiral_restr0.0850.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026765
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021329
X-RAY DIFFRACTIONr_nbd_refined0.2020.21076
X-RAY DIFFRACTIONr_nbd_other0.2430.26494
X-RAY DIFFRACTIONr_nbtor_other0.0840.23811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2272
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4490.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.220
X-RAY DIFFRACTIONr_mcbond_it0.7271.53684
X-RAY DIFFRACTIONr_mcangle_it1.36625929
X-RAY DIFFRACTIONr_scbond_it1.89732444
X-RAY DIFFRACTIONr_scangle_it3.2424.52374
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 158
Rwork0.237 2474
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)
13.28631.2260.46172.92740.73171.1377-0.00860.0848-0.17050.0215-0.15920.22910.0624-0.1650.16770.08220.03440.00420.1047-0.07490.15049.994822.614158.6478
21.96650.3041-0.20162.5361-0.07771.6558-0.0265-0.0541-0.07270.11440.0483-0.1525-0.04740.0408-0.02190.09930.06870.00490.091-0.02670.091831.01226.450666.0356
31.623-0.21560.25781.31750.26671.42650.021-0.150.20020.10080.0844-0.21250.0250.1553-0.10540.08250.0176-0.00260.1049-0.11990.196727.879951.308979.1532
42.5601-0.77451.22391.3545-0.53481.3674-0.0354-0.30220.01460.07430.21310.22270.1005-0.1092-0.17780.11110.0170.04170.0816-0.03550.15723.982952.773281.8998
52.6754-0.1547-0.18412.30370.95212.682-0.044-0.04250.1216-0.00780.00450.2943-0.0923-0.42010.03950.12440.11740.08260.26080.09640.083216.95732.127828.5182
62.5423-0.01211.06560.8416-0.13534.0817-0.10630.02530.13890.01810.0936-0.0011-0.31510.30870.01260.21830.05690.0530.17230.00490.016235.480643.541533.9994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1272 - 127
2X-RAY DIFFRACTION2BB2 - 1272 - 127
3X-RAY DIFFRACTION3CC2 - 1282 - 128
4X-RAY DIFFRACTION4DD2 - 1402 - 140
5X-RAY DIFFRACTION5EE2 - 1262 - 126
6X-RAY DIFFRACTION6FF2 - 1272 - 127
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.35
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6.26
X-RAY DIFFRACTIONr_plane_restr0.005

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