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- PDB-1vrm: Crystal structure of the apbe protein (tm1553) from thermotoga ma... -

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Basic information

Entry
Database: PDB / ID: 1vrm
TitleCrystal structure of the apbe protein (tm1553) from thermotoga maritima msb8 at 1.58 A resolution
Componentshypothetical protein TM1553Hypothesis
KeywordsBIOSYNTHETIC PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


protein flavinylation / FAD:protein FMN transferase / FAD binding / transferase activity / membrane => GO:0016020 / metal ion binding
Similarity search - Function
T-fold / ApbE-like superfamily / T-fold / ApbE-like domains / Flavin transferase ApbE / ApbE family / ApbE-like superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / : / FAD:protein FMN transferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution.
Authors: Han, G.W. / Sri Krishna, S. / Schwarzenbacher, R. / McMullan, D. / Ginalski, K. / Elsliger, M.A. / Brittain, S.M. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H. / ...Authors: Han, G.W. / Sri Krishna, S. / Schwarzenbacher, R. / McMullan, D. / Ginalski, K. / Elsliger, M.A. / Brittain, S.M. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H. / Canaves, J.M. / Chiu, H.J. / DiDonato, M. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Miller, M.D. / Morse, A.T. / Moy, K. / Nigoghossian, E. / Oommachen, S. / Ouyang, J. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Wang, X. / West, B. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Remark 999 SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED ... SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 40-352 OF THE PREDICTED TM1553 GENE PRODUCT. IN ORDER TO REMOVE A PREDICTED TRANSMEMBRANE HELIX, THE FIRST 39 RESIDUES WERE NOT INCLUDED IN THE CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM1553
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2575
Polymers36,9031
Non-polymers3554
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.742, 76.946, 86.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein TM1553 / Hypothesis


Mass: 36902.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1553 / Production host: Escherichia coli (E. coli) / References: GenBank: 15644301, UniProt: Q9X1N9*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.37 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 10.0% MPD, 0.1M Citrate pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97950,1.00003
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.000031
ReflectionResolution: 1.5→20.61 Å / Num. obs: 51395 / % possible obs: 96.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.58-1.6273.51.70.7030.928170.703
1.62-1.6784.81.90.592131810.592
1.67-1.7193.82.10.4941.334490.494
1.71-1.7797.82.60.421.435170.42
1.77-1.8299.13.10.3272.134560.327
1.82-1.8999.93.40.2712.533870.271
1.89-1.961003.60.219132770.219
1.96-2.041003.60.1594.431510.159
2.04-2.131003.60.1374.330420.137
2.13-2.231003.60.1126.328940.112
2.23-2.361003.60.1052.727810.105
2.36-2.51003.60.0957.525980.095
2.5-2.671003.60.0838.224910.083
2.67-2.881003.60.0739.423170.073
2.88-3.1699.93.60.06510.121250.065
3.16-3.5399.83.60.0561119290.056
3.53-4.0899.63.60.04912.917190.049
4.08-599.33.50.04314.314650.043
5-7.07993.40.05810.811590.058
7.07-20.61943.10.0511.56400.05

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→20.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.375 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE ADDITIONAL DENSITY IN THE POCKET NEAR HIS 276 HAS BEEN MODELED AS AN UNL, UNKNOWN LIGAND. RESIDUES WHICH INTERACT WITH THE UNL ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE ADDITIONAL DENSITY IN THE POCKET NEAR HIS 276 HAS BEEN MODELED AS AN UNL, UNKNOWN LIGAND. RESIDUES WHICH INTERACT WITH THE UNL (INCLUDING ALA-259, THR-260, SER-261, HIS-276 AND ASP-303) ARE CONSERVED IN PSI-BLAST RESULT.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2622 5.1 %RANDOM
Rwork0.157 ---
all0.159 ---
obs-48704 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 39 400 2852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222528
X-RAY DIFFRACTIONr_bond_other_d0.0010.022352
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9623434
X-RAY DIFFRACTIONr_angle_other_deg0.88735442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87223.661112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6415425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0041516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02529
X-RAY DIFFRACTIONr_nbd_refined0.2430.2519
X-RAY DIFFRACTIONr_nbd_other0.1840.22420
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21281
X-RAY DIFFRACTIONr_nbtor_other0.0850.21527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2319
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.234
X-RAY DIFFRACTIONr_mcbond_it2.87231652
X-RAY DIFFRACTIONr_mcbond_other0.6043637
X-RAY DIFFRACTIONr_mcangle_it3.20652504
X-RAY DIFFRACTIONr_scbond_it5.54981095
X-RAY DIFFRACTIONr_scangle_it7.32711929
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 144 -
Rwork0.255 2654 -
obs--71.78 %

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