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- PDB-4ap8: Crystal structure of human Molybdopterin synthase catalytic subun... -

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Basic information

Entry
Database: PDB / ID: 4ap8
TitleCrystal structure of human Molybdopterin synthase catalytic subunit (MOCS2B)
ComponentsMOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
KeywordsTRANSFERASE
Function / homology
Function and homology information


: / molybdopterin synthase / molybdopterin synthase activity / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / Mo-molybdopterin cofactor biosynthetic process / nuclear speck / nucleoplasm / cytosol
Similarity search - Function
Molybdopterin synthase catalytic subunit, eukaryotes / 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
Molybdopterin synthase catalytic subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsVollmar, M. / Kiyani, W. / Krojer, T. / Goubin, S. / Allerston, C. / Froese, D.S. / von Delft, F. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. ...Vollmar, M. / Kiyani, W. / Krojer, T. / Goubin, S. / Allerston, C. / Froese, D.S. / von Delft, F. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Human Molybdopterin Synthase Catalytic Subunit (Mocs2B)
Authors: Vollmar, M. / Kiyani, W. / Krojer, T. / Goubin, S. / Allerston, C. / Froese, D.S. / von Delft, F. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W.W.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations
Revision 1.2Jun 5, 2013Group: Derived calculations
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 / _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 SYNTHASE CATALYTIC SUBUNIT
B: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
C: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
D: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,86610
Polymers60,3744
Non-polymers4936
Water1,67593
1
A: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules

D: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4956
Polymers30,1872
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_574-x+y,-x+2,z-1/31
Buried area3550 Å2
ΔGint-3.1 kcal/mol
Surface area12360 Å2
MethodPISA
2
D: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules

A: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4956
Polymers30,1872
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z+1/31
Buried area3550 Å2
ΔGint-3.1 kcal/mol
Surface area12360 Å2
MethodPISA
3
B: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules

C: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3714
Polymers30,1872
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area3240 Å2
ΔGint-8.6 kcal/mol
Surface area12380 Å2
MethodPISA
4
C: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules

B: MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3714
Polymers30,1872
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
Buried area3240 Å2
ΔGint-8.6 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.968, 138.968, 159.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT / MOCO1-B / MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2 LARGE SUBUNIT / MOLYBDENUM COFACTOR SYNTHESIS ...MOCO1-B / MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2 LARGE SUBUNIT / MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2B / MOCS2B / MOLYBDOPTERIN-SYNTHASE LARGE SUBUNIT / MPT SYNTHASE LARGE SUBUNIT


Mass: 15093.410 Da / Num. of mol.: 4 / Fragment: CATALYTIC SUBUNIT RESIDUES 38-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O96007, molybdopterin synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 6.28 Å3/Da / Density % sol: 80.42 % / Description: NONE
Crystal growDetails: 0.1M HEPES PH 7.3, 0.8M POTASSIUM/SODIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.78→159.57 Å / Num. obs: 45153 / % possible obs: 99.8 % / Observed criterion σ(I): 2.2 / Redundancy: 4.3 % / Biso Wilson estimate: 86.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QIE

2qie


Resolution: 2.78→96.09 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 14.001 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19932 2275 5 %RANDOM
Rwork0.17158 ---
obs0.17296 42841 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å21.59 Å20 Å2
2--3.18 Å20 Å2
3----4.77 Å2
Refinement stepCycle: LAST / Resolution: 2.78→96.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 32 93 4230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194229
X-RAY DIFFRACTIONr_bond_other_d0.0070.022812
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9645742
X-RAY DIFFRACTIONr_angle_other_deg1.4836911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55824.268164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46715722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1181521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214619
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02814
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 163 -
Rwork0.365 2915 -
obs--99.87 %
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)
14.18150.85671.40681.5343-0.6463.6162-0.31080.284-0.221-0.15520.1704-0.13340.00830.29260.14040.21030.0687-0.01250.15060.02370.087-0.3173146.915.9759
22.4453-0.40240.6650.8345-0.15563.059-0.2244-0.0809-0.02170.18080.06950.0556-0.0614-0.01170.15490.18570.0646-0.02920.0870.04580.0714-4.1278150.281512.3133
33.4131-1.9073-0.22153.39680.27661.4273-0.4565-0.33470.1730.77570.3511-0.261-0.11950.35530.10540.36560.1533-0.05420.19830.01570.0348-26.6996173.227620.2135
41.5111-2.12410.43263.0115-0.44252.8228-0.2914-0.1538-0.06190.40610.20660.05220.02670.07610.08480.20950.12640.00630.10960.03220.1231-26.2075169.305113.5708
51.499-0.241-0.55663.0811-1.07872.0059-0.00190.0067-0.0309-0.184-0.2312-0.02350.15250.17210.23320.26140.20540.03230.18550.04010.04095.8454127.657528.968
66.3659-0.8033-7.05933.41594.423211.59290.5455-0.8677-0.0355-0.2206-0.3908-0.2384-0.70290.3638-0.15480.28050.15390.13830.3790.17950.186215.2502119.489235.254
70.27060.2581-0.85587.4966-0.28822.7620.05090.0191-0.01370.1845-0.11050.2368-0.167-0.13490.05960.29870.0987-0.02010.24460.01490.07663.617136.502937.0173
80.28130.4430.15151.85921.6883.5076-0.03280.02010.117-0.47150.03450.0442-0.45680.1237-0.00180.31820.00630.01610.2108-0.00430.078610.1055161.444541.845
90.59450.12480.01452.20811.83452.98040.0090.00910.005-0.2296-0.16360.18220.0883-0.19540.15450.18560.0196-0.03450.1952-0.04630.02275.5234156.891942.8528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 91
2X-RAY DIFFRACTION2A92 - 171
3X-RAY DIFFRACTION3B38 - 93
4X-RAY DIFFRACTION4B94 - 171
5X-RAY DIFFRACTION5C38 - 144
6X-RAY DIFFRACTION6C145 - 151
7X-RAY DIFFRACTION7C152 - 171
8X-RAY DIFFRACTION8D40 - 99
9X-RAY DIFFRACTION9D100 - 172

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