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- PDB-1y80: Structure of a corrinoid (factor IIIm)-binding protein from Moore... -

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Basic information

Entry
Database: PDB / ID: 1y80
TitleStructure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica
ComponentsPredicted cobalamin binding protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / corrinoid / factor IIIm / methyl transferase / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / methanogenesis / cobalamin binding / cobalt ion binding / methylation
Similarity search - Function
Methyltransferase cognate corrinoid protein / B12-binding N-terminal domain profile. / B12 binding domain / : / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily ...Methyltransferase cognate corrinoid protein / B12-binding N-terminal domain profile. / B12 binding domain / : / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CO-5-METHOXYBENZIMIDAZOLYLCOBAMIDE / : / 5-methyltetrahydrofolate--homocysteine S-methyltransferase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 1.7 Å
AuthorsLiu, Z.-J. / Fu, Z.-Q. / Tempel, W. / Das, A. / Habel, J. / Zhou, W. / Chang, J. / Chen, L. / Lee, D. / Nguyen, D. ...Liu, Z.-J. / Fu, Z.-Q. / Tempel, W. / Das, A. / Habel, J. / Zhou, W. / Chang, J. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Ljungdahl, L. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica
Authors: Liu, Z.-J. / Fu, Z.-Q. / Tempel, W. / Das, A. / Habel, J. / Zhou, W. / Chang, J. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Ljungdahl, L. / Rose, J.P. / Wang, B.-C.
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6787
Polymers22,3471
Non-polymers1,3316
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.689, 62.738, 34.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsnot known

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Components

#1: Protein Predicted cobalamin binding protein / corrinoid (factor IIIm)-binding protein


Mass: 22346.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria) / References: GenBank: 49235916, UniProt: Q2RJ67*PLUS
#2: Chemical ChemComp-B1M / CO-5-METHOXYBENZIMIDAZOLYLCOBAMIDE / FACTOR IIIM


Mass: 1331.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H86CoN13O15P
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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

Crystal growTemperature: 291 K / Method: modified microbatch / pH: 6.7
Details: 0.1M Sodium HEPES, 1.6M ammonium sulfate, 30% 1,6-hexanediol, pH 6.7, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5798 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5798 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 13939 / Rmerge(I) obs: 0.077
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.660.216138.6
1.66-1.720.195160.3
1.72-1.80.165189.1
1.8-1.90.137192.3
1.9-2.020.114193.4
2.02-2.170.094194.2
2.17-2.390.087187.8
2.39-2.740.08196.2
2.74-3.450.072197.4
3.45-500.064189.3

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.15 Å / D res low: 62.652 Å / FOM : 0.29 / Reflection: 6706
Phasing MAD shell
Resolution (Å)FOM Reflection
7.82-62.6520.33348
4.91-7.820.38581
3.83-4.910.37730
3.24-3.830.37837
2.86-3.240.31875
2.59-2.860.291024
2.38-2.590.241124
2.22-2.380.171187
Phasing dmFOM : 0.56 / FOM acentric: 0.58 / FOM centric: 0.48 / Reflection: 6706 / Reflection acentric: 5548 / Reflection centric: 1158
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.1-41.5510.850.850.63338197141
3.8-6.10.770.820.63939705234
3.1-3.80.720.750.581141929212
2.7-3.10.580.60.461068906162
2.3-2.70.460.480.3419961732264
2.2-2.30.340.350.2512241079145

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Processing

Software
NameVersionClassificationNB
SOLVE2.02phasing
RESOLVE2.02phasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→41.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.945 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 528 4.2 %RANDOM
Rwork0.17425 ---
obs0.1757 12184 91.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.075 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---1.09 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 96 72 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221031
X-RAY DIFFRACTIONr_bond_other_d0.0030.02987
X-RAY DIFFRACTIONr_angle_refined_deg1.9542.121422
X-RAY DIFFRACTIONr_angle_other_deg0.75332290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9295124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.3226.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93815170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.964152
X-RAY DIFFRACTIONr_chiral_restr0.0670.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02189
X-RAY DIFFRACTIONr_nbd_refined0.2050.2188
X-RAY DIFFRACTIONr_nbd_other0.1710.21067
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2497
X-RAY DIFFRACTIONr_nbtor_other0.0810.2561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8612674
X-RAY DIFFRACTIONr_mcbond_other0.4662261
X-RAY DIFFRACTIONr_mcangle_it2.2993989
X-RAY DIFFRACTIONr_scbond_it2.0772456
X-RAY DIFFRACTIONr_scangle_it3.0293433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 34 -
Rwork0.214 719 -
obs--73.61 %

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