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- PDB-1o4t: Crystal structure of a predicted oxalate decarboxylase (tm1287) f... -

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Basic information

Entry
Database: PDB / ID: 1o4t
TitleCrystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution
Componentsputative oxalate decarboxylase
KeywordsLYASE / Double-stranded beta-helix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


oxalate decarboxylase activity / oxalate metabolic process / manganese ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / OXALATE ION / Oxalate-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution
Authors: Schwarzenbacher, R. / von Delft, F. / Jaroszewski, L. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. ...Authors: Schwarzenbacher, R. / von Delft, F. / Jaroszewski, L. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJul 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative oxalate decarboxylase
B: putative oxalate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7886
Polymers29,5022
Non-polymers2864
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-33 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.132, 49.738, 69.547
Angle α, β, γ (deg.)90.00, 123.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein putative oxalate decarboxylase


Mass: 14750.821 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1287 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X113
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.55 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / pH: 6
Details: 20 % PEG 6000, 1.0 M LiCl, 0.1 M MES, pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.00
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mlsatTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
410 mg/mlprotein1drop
520 %PEG60001reservoir
61.0 M1reservoirLiCl
70.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.983967
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2002 / Details: FLAT MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983967 Å / Relative weight: 1
ReflectionResolution: 1.95→25.29 Å / Num. obs: 17758 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 36.93 Å2 / Rsym value: 0.083 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.555 / % possible all: 88
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 33.52 Å / % possible obs: 0.098 % / Num. measured all: 62794
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FI2

1fi2


Resolution: 1.95→25.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.542 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. METAL IDENTIFIED BY A) HOMOLOGY TO 1J58 B) BEST AGREEMENT OF REFINED B-FACTOR WITH LIGATING RESIDUES. 2. OXALATE IDENIFIED BASED ON HOMOLOGY TO 1J58. HIGH BFACTORS INDICATE PARTIAL ...Details: 1. METAL IDENTIFIED BY A) HOMOLOGY TO 1J58 B) BEST AGREEMENT OF REFINED B-FACTOR WITH LIGATING RESIDUES. 2. OXALATE IDENIFIED BASED ON HOMOLOGY TO 1J58. HIGH BFACTORS INDICATE PARTIAL OCCUPANCY, WHICH WAS NOT MODELED. C- C BOND PLANARITY WAS NOT RESTRAINED DURING REFINEMENT. 3. ARG23 HAS CLOSELY-BOUND WATER; DENSITY SUGGESTS POSSIBLE OMEGA -HYDROXYLATED ARGININE. 4. UNEXPLAINED CONTINUOUS DENSITY MODELED AS WATER CHAINS. 5. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 883 5 %RANDOM
Rwork0.16 ---
obs0.163 16875 95.2 %-
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: 32.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å21.66 Å2
2---0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 14 198 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211823
X-RAY DIFFRACTIONr_bond_other_d0.010.021667
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9622450
X-RAY DIFFRACTIONr_angle_other_deg0.84933887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59524.07481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12615330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7331511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.190.2304
X-RAY DIFFRACTIONr_nbd_other0.1870.21650
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.51136
X-RAY DIFFRACTIONr_mcangle_it1.48321823
X-RAY DIFFRACTIONr_scbond_it2.6753687
X-RAY DIFFRACTIONr_scangle_it4.4744.5627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 63
Rwork0.287 1078
Refinement TLS params.Method: refined / Origin x: 15.3219 Å / Origin y: -0.1822 Å / Origin z: 16.2354 Å
111213212223313233
T-0.1642 Å2-0.0243 Å2-0.0371 Å2--0.18 Å2-0.0053 Å2---0.1254 Å2
L2.4919 °21.1049 °2-1.9792 °2-1.25 °2-1.8341 °2--4.4463 °2
S-0.1108 Å °0.2669 Å °-0.0363 Å °-0.1352 Å °0.1837 Å °0.0443 Å °-0.0197 Å °-0.2088 Å °-0.0729 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 12119 - 133
2X-RAY DIFFRACTION1BB7 - 12119 - 133
Software
*PLUS
Name: REFMAC / Version: 5.1.9999 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 33.52 Å / Num. reflection obs: 17758 / % reflection Rfree: 5 % / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.57
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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