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- PDB-2ah6: Crystal structure of a putative cobalamin adenosyltransferase (bh... -

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Basic information

Entry
Database: PDB / ID: 2ah6
TitleCrystal structure of a putative cobalamin adenosyltransferase (bh1595) from bacillus halodurans c-125 at 1.60 A resolution
ComponentsBH1595, unknown conserved protein
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding
Similarity search - Function
Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (10174212) from BACILLUS HALODURANS at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THERE IS A CLONING ARTIFACT AT RESIDUE 42 IN THE SEQUENCE DATABASE REFERENCE. THE DENSITY ...SEQUENCE THERE IS A CLONING ARTIFACT AT RESIDUE 42 IN THE SEQUENCE DATABASE REFERENCE. THE DENSITY FOR THIS RESIDUE IN EACH MONOMER SUGGESTS THAT IT IS SERINE AND NOT LEUCINE. SEQUENCING OF THE CONSTRUCT CONFIRMED THAT THIS RESIDUE IS SERINE IN THE EXPRESSED PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH1595, unknown conserved protein
B: BH1595, unknown conserved protein
C: BH1595, unknown conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4689
Polymers72,0963
Non-polymers3726
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-20 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.610, 84.380, 113.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA24 - 7636 - 88
21ASPASPLEULEUBB24 - 7636 - 88
31ASPASPLEULEUCC24 - 7636 - 88
42PROPROGLUGLUAA83 - 10495 - 116
52PROPROGLUGLUBB83 - 10495 - 116
62PROPROGLUGLUCC83 - 10495 - 116
73LEULEUGLUGLUAA108 - 180120 - 192
83LEULEUGLUGLUBB108 - 180120 - 192
93LEULEUGLUGLUCC108 - 180120 - 192

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Components

#1: Protein BH1595, unknown conserved protein


Mass: 24031.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: 10174212 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KCH6
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 277 K / pH: 6.9
Details: 0.2M K2NO3, 20.0% PEG-3350, No Buffer pH 6.9 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 3, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 68629 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Χ2: 0.985
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
1.6-1.6399.93.60.59134261.0621
1.63-1.661003.60.50733521.0551
1.66-1.6999.93.60.45433980.9931
1.69-1.7299.93.60.40334250.9551
1.72-1.761003.70.3533400.9821
1.76-1.81003.70.334031.0821
1.8-1.851003.70.25634251.0881
1.85-1.91003.70.21233740.9171
1.9-1.951003.70.18234100.9421
1.95-2.021003.70.15134091.0521
2.02-2.091003.70.13334210.9471
2.09-2.171003.70.11134270.9491
2.17-2.271003.70.09834160.9181
2.27-2.391003.70.08934251.0611
2.39-2.541003.70.08534291.0521
2.54-2.741003.70.0834760.9731
2.74-3.0199.93.70.06834630.911
3.01-3.451003.70.05534941.0221
3.45-4.3499.73.70.04335200.9591
4.34-5096.93.50.0335960.7791

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
PHASERphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: molecular replacement
Starting model: 1RTY

1rty


Resolution: 1.6→29.02 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.003 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1)HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2)SIGNIFICANT DIFFERENCE ELECTRON DENSITY OF UNKNOWN ORIGIN IS ADJACENT TO A106 IN THE MODEL. 3)THREE NITRATE ANIONS FROM THE ...Details: 1)HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2)SIGNIFICANT DIFFERENCE ELECTRON DENSITY OF UNKNOWN ORIGIN IS ADJACENT TO A106 IN THE MODEL. 3)THREE NITRATE ANIONS FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 3503 5.1 %RANDOM
Rwork0.15 ---
all0.152 ---
obs-65054 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 24 549 4308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223887
X-RAY DIFFRACTIONr_bond_other_d0.0010.023600
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9655270
X-RAY DIFFRACTIONr_angle_other_deg0.87438297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7825489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91623.586198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83915654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2081538
X-RAY DIFFRACTIONr_chiral_restr0.0950.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_nbd_refined0.2330.2939
X-RAY DIFFRACTIONr_nbd_other0.1820.23858
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22006
X-RAY DIFFRACTIONr_nbtor_other0.0810.22256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2393
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.223
X-RAY DIFFRACTIONr_mcbond_it1.93932457
X-RAY DIFFRACTIONr_mcbond_other0.543976
X-RAY DIFFRACTIONr_mcangle_it2.82353866
X-RAY DIFFRACTIONr_scbond_it4.49781575
X-RAY DIFFRACTIONr_scangle_it6.381111397
Refine LS restraints NCS

Ens-ID: 1 / Number: 2101 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.645
2BLOOSE POSITIONAL1.055
3CLOOSE POSITIONAL0.615
1ALOOSE THERMAL2.1810
2BLOOSE THERMAL2.410
3CLOOSE THERMAL2.1310
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 280 -
Rwork0.248 4767 -
obs--99.88 %
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)
11.34440.0821-0.42241.50260.61361.9203-0.0083-0.0821-0.09020.2814-0.05030.07470.12950.01330.0586-0.16070.00190.0176-0.1552-0.0117-0.187220.23974.44222.411
21.0607-0.0935-0.36971.27880.10861.4451-0.021-0.0102-0.0470.02530.015-0.1182-0.0570.12660.006-0.2111-0.01530.009-0.1383-0.0341-0.192438.57273.8986.997
31.35960.0366-0.39651.75470.14231.36930.1168-0.07670.22070.0133-0.011-0.028-0.27050.0353-0.1058-0.09010.00630.0299-0.152-0.0214-0.159329.00596.65114.426
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA24 - 7636 - 88
21AA83 - 18095 - 192
32BB19 - 18031 - 192
43CC23 - 18435 - 196

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