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- PDB-1zgh: Methionyl-tRNA formyltransferase from Clostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 1zgh
TitleMethionyl-tRNA formyltransferase from Clostridium thermocellum
ComponentsMethionyl-tRNA formyltransferase
KeywordsTRANSFERASE / Methionyl-tRNA formyltransferase / Southeast Collaboratory for Structural Genomics / Clostridium thermocellum / PSI / Protein Structure Initiative / SECSG
Function / homology
Function and homology information


hydroxymethyl-, formyl- and related transferase activity / biosynthetic process
Similarity search - Function
Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 - #20 / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 2.05 Å
AuthorsYang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. ...Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Lee, D. / Lin, D. / Chang, S. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Wang, B. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Methionyl-tRNA formyltransferase from Clostridium thermocellum
Authors: Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Lee, D. / Lin, D. / Chang, S. / Arendall III, W.B. / Richardson, J.S. / ...Authors: Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Lee, D. / Lin, D. / Chang, S. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Wang, B. / Southeast Collaboratory for Structural Genomics
History
DepositionApr 21, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionMay 3, 2005ID: 1XG9
Revision 1.0May 3, 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S).AUTHOR STATES THAT 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: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)30,35518
Polymers30,3551
Non-polymers017
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.396, 85.396, 104.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Methionyl-tRNA formyltransferase /


Mass: 30354.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Plasmid: pET-15g / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 48859327, UniProt: A3DHJ7*PLUS
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 298 K / Method: modified microbatch / pH: 5.6
Details: 2.5M amonium sulfate, 0.1M sodium citrate, pH 5.6, modified microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 27555 / % possible obs: 98.3 % / Rmerge(I) obs: 0.118 / Χ2: 2.194
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2Diffraction-ID% possible all
1.98-2.050.53522950.836183.6
2.05-2.130.45427380.872199.9
2.13-2.230.39327500.9711100
2.23-2.350.36327511.0591100
2.35-2.490.3227661.2131100
2.49-2.690.25727891.3551100
2.69-2.960.18627911.7931100
2.96-3.390.11828112.6571100
3.39-4.260.08728473.931100
4.26-500.07630174.725199.4

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.5 Å / D res low: 20 Å / FOM : 0.4 / Reflection: 13589
Phasing MAD shell
Resolution (Å)FOM Reflection
8.52-200.39766
5.54-8.520.421195
4.38-5.540.41471
3.74-4.380.381720
3.31-3.740.411903
3-3.310.422065
2.77-30.42189
2.58-2.770.362280
Phasing dmFOM : 0.58 / FOM acentric: 0.59 / FOM centric: 0.51 / Reflection: 17127 / Reflection acentric: 14644 / Reflection centric: 2483
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-19.7570.890.890.65813525288
4.1-6.60.840.880.724391917522
3.3-4.10.790.810.6529682489479
2.9-3.30.680.710.529342553381
2.5-2.90.490.510.3250024459543
2.3-2.50.140.140.1729712701270

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: SAS / Resolution: 2.05→30.192 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.213 / SU B: 6.361 / SU ML: 0.088 / SU R Cruickshank DPI: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; arp/warp,molprobity were also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1222 4.924 %RANDOM
Rwork0.2086 ---
all0.21 ---
obs-24816 99.919 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.132 Å20 Å20 Å2
2---0.132 Å20 Å2
3---0.264 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 17 47 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221850
X-RAY DIFFRACTIONr_bond_other_d0.0010.021696
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9612501
X-RAY DIFFRACTIONr_angle_other_deg0.81633942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59724.45883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.467159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
X-RAY DIFFRACTIONr_nbd_refined0.2040.2280
X-RAY DIFFRACTIONr_nbd_other0.170.21527
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2894
X-RAY DIFFRACTIONr_nbtor_other0.0780.21020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.29
X-RAY DIFFRACTIONr_mcbond_it1.2661.51267
X-RAY DIFFRACTIONr_mcbond_other0.2631.5459
X-RAY DIFFRACTIONr_mcangle_it1.42921838
X-RAY DIFFRACTIONr_mcangle_other0.6421536
X-RAY DIFFRACTIONr_scbond_it2.5713799
X-RAY DIFFRACTIONr_scbond_other0.74131533
X-RAY DIFFRACTIONr_scangle_it3.6184.5663
X-RAY DIFFRACTIONr_scangle_other1.5944.52406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.1030.214950.1931687178599.832
2.103-2.1610.214780.18916761754100
2.161-2.2230.253760.18416191695100
2.223-2.2910.207700.18615751645100
2.291-2.3660.18850.1911544163099.939
2.366-2.4480.257830.20114781561100
2.448-2.540.264800.2021409149099.933
2.54-2.6430.196750.20913761451100
2.643-2.7590.27700.21713371407100
2.759-2.8930.32670.22612651332100
2.893-3.0480.234610.2171219128199.922
3.048-3.2310.274560.21511481204100
3.231-3.4510.196520.2211091161100
3.451-3.7230.233580.20510071065100
3.723-4.0720.206580.1899481006100
4.072-4.5430.192460.169861907100
4.543-5.2260.212350.174778813100
5.226-6.3530.299390.266667706100
6.353-8.7920.334200.289551571100
8.792-30.1920.284180.29734037296.237
Refinement TLS params.Method: refined / Origin x: 33.312 Å / Origin y: 27.772 Å / Origin z: 31.685 Å
111213212223313233
T-0.1195 Å2-0.0019 Å20.0125 Å2--0.0147 Å2-0.0809 Å2---0.0149 Å2
L2.3432 °20.7518 °21.4324 °2-1.102 °20.5919 °2--1.6793 °2
S0.0033 Å °0.4368 Å °-0.197 Å °-0.1504 Å °0.0586 Å °0.0705 Å °0.1719 Å °0.0216 Å °-0.0619 Å °
Refinement TLS groupSelection: ALL

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