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- PDB-3s0m: A Structural Element that Modulates Proton-Coupled Electron Trans... -

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Basic information

Entry
Database: PDB / ID: 3s0m
TitleA Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase
ComponentsOxalate decarboxylase oxdC
KeywordsLYASE / bicupin
Function / homology
Function and homology information


oxalate decarboxylase / oxalate decarboxylase activity / oxalate metabolic process / outer membrane-bounded periplasmic space / metal ion binding / cytoplasm
Similarity search - Function
Bicupin, oxalate decarboxylase/oxidase / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CARBONATE ION / : / DI(HYDROXYETHYL)ETHER / Oxalate decarboxylase OxdC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsSaylor, B.T. / Reinhardt, L.A. / Lu, Z. / Shukla, M.S. / Cleland, W.W. / Allen, K.N. / Richards, N.G.J.
CitationJournal: Biochemistry / Year: 2012
Title: A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.
Authors: Saylor, B.T. / Reinhardt, L.A. / Lu, Z. / Shukla, M.S. / Nguyen, L. / Cleland, W.W. / Angerhofer, A. / Allen, K.N. / Richards, N.G.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_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.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_ref_seq_dif.details / _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: Oxalate decarboxylase oxdC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1308
Polymers42,6681
Non-polymers4627
Water6,305350
1
A: Oxalate decarboxylase oxdC
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)258,78048
Polymers256,0066
Non-polymers2,77342
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area50410 Å2
ΔGint-284 kcal/mol
Surface area71460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.761, 154.761, 121.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Oxalate decarboxylase oxdC


Mass: 42667.746 Da / Num. of mol.: 1 / Mutation: T165V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subsp. subtilis str. 168 / Gene: BSU33240, oxalate decarboxylase, oxdC, yvrK / Plasmid: PET15B-T165V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O34714, oxalate decarboxylase

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v polyethylene glycol 6000, 2 M aq. NaCl , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 25, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.31→23.61 Å / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.68 % / Rmerge(I) obs: 0.1861 / Rsym value: 0.2635 / Net I/σ(I): 5.43
Reflection shellResolution: 2.31→2.4 Å / Redundancy: 4.07 % / Rmerge(I) obs: 0.4735 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.4326 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
SAINTdata reduction
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→23.61 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.3 / σ(F): 0 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 3353 8.06 %
Rwork0.1856 --
obs0.1912 41624 87.53 %
all-47554 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.239 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.0557 Å20 Å20 Å2
2---8.0557 Å2-0 Å2
3---4.8283 Å2
Refinement stepCycle: LAST / Resolution: 2.31→23.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 25 350 3388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073114
X-RAY DIFFRACTIONf_angle_d1.0234218
X-RAY DIFFRACTIONf_dihedral_angle_d13.8021144
X-RAY DIFFRACTIONf_chiral_restr0.072444
X-RAY DIFFRACTIONf_plane_restr0.003554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3101-2.3430.29881150.27571339X-RAY DIFFRACTION74
2.343-2.3780.311340.25361471X-RAY DIFFRACTION82
2.378-2.41510.30671430.24071566X-RAY DIFFRACTION86
2.4151-2.45470.38551400.2331648X-RAY DIFFRACTION88
2.4547-2.49690.31631410.22911574X-RAY DIFFRACTION88
2.4969-2.54230.32071390.2381593X-RAY DIFFRACTION89
2.5423-2.59110.32381370.23461618X-RAY DIFFRACTION89
2.5911-2.6440.28961400.22311601X-RAY DIFFRACTION87
2.644-2.70140.33221380.22331571X-RAY DIFFRACTION86
2.7014-2.76410.27811360.22731542X-RAY DIFFRACTION85
2.7641-2.83310.27681220.21311510X-RAY DIFFRACTION83
2.8331-2.90960.29631340.22931548X-RAY DIFFRACTION84
2.9096-2.9950.28051310.2031494X-RAY DIFFRACTION83
2.995-3.09150.31771420.18641503X-RAY DIFFRACTION82
3.0915-3.20180.25411370.17141567X-RAY DIFFRACTION87
3.2018-3.32960.22061430.16751603X-RAY DIFFRACTION88
3.3296-3.48070.22261370.15981610X-RAY DIFFRACTION88
3.4807-3.66360.25781340.17211556X-RAY DIFFRACTION85
3.6636-3.89220.21941330.1661623X-RAY DIFFRACTION88
3.8922-4.19110.18021500.12191683X-RAY DIFFRACTION93
4.1911-4.61010.17531480.11991708X-RAY DIFFRACTION93
4.6101-5.27070.1481580.10131775X-RAY DIFFRACTION98
5.2707-6.61620.21551570.14361775X-RAY DIFFRACTION98
6.6162-23.61420.18761640.15111793X-RAY DIFFRACTION98
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)
10.00040.00020.00040.0003-0.00010.00060.00050.0002-0.00380.0034-0.0031-0.00410.00190.004200.0144-0.00080.00230.0346-0.00870.0182-31.5312-24.9591-68.3621
20.00460.0020.00220.0125-0.00110.0172-0.0024-0.0042-0.00050.0048-0.0122-0.0019-0.00360.0031-0.0697-0.00050.0013-0.01170.0060.016-0.002-4.1528-25.0859-46.461
30.00160.0022-0.00260.0048-0.00460.0044-0.00430.0002-0.0002-0.0009-0.0001-0.0031-0.00450.0028-0.00470.01490.0071-0.00630.01140.00710.010917.4828-28.3122-45.0978
40.0029-0.00240.00290.0051-0.00370.0063-0.0006-0.00190.00130.00060.00060.0033-0.0026-0.0011-0.00450.0455-0.00110.00270.03030.02180.0234-3.7209-22.9156-27.0165
50.01040.0044-0.00430.0134-0.00670.01770.0055-0.00440.00250.00460.00330.0037-0.0048-0.00210.0350.00020.00880.01060.00310.0050.007-19.1291-15.7509-42.2427
600-0.00010.0005-0.00070.00070.00190.00340.00590.00120.00330.0033-0.0034-0.00770.00780.02520.00420.0210.02520.00940.028-36.7511-7.9984-35.6364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:24)
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:155)
3X-RAY DIFFRACTION3chain 'A' and (resseq 156:213)
4X-RAY DIFFRACTION4chain 'A' and (resseq 214:240)
5X-RAY DIFFRACTION5chain 'A' and (resseq 241:353)
6X-RAY DIFFRACTION6chain 'A' and (resseq 354:382)

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