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- PDB-4pzu: Crystal structure of a putative uncharacterize protein Rv3404c an... -

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Basic information

Entry
Database: PDB / ID: 4pzu
TitleCrystal structure of a putative uncharacterize protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis
ComponentsUncharacterized protein Rv3404c/MT3512
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Diseases / uncharacterized protein / identified drug target / integrated gene co-expression network analysis / Mtb / cell wall biogenesis
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / conversion of methionyl-tRNA to N-formyl-methionyl-tRNA / hydroxymethyl-, formyl- and related transferase activity / methionyl-tRNA formyltransferase activity / biosynthetic process / carbohydrate metabolic process / protein homodimerization activity / cytosol
Similarity search - Function
N-formyltransferase dimerization C-terminal domain / N-formyltransferase dimerization C-terminal domain / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
dTDP-4-amino-4,6-dideoxyglucose formyltransferase / dTDP-4-amino-4,6-dideoxyglucose formyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative uncharacterize protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis
Authors: Edwards, T.E. / Dranow, D.M.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Rv3404c/MT3512
B: Uncharacterized protein Rv3404c/MT3512
C: Uncharacterized protein Rv3404c/MT3512
D: Uncharacterized protein Rv3404c/MT3512
E: Uncharacterized protein Rv3404c/MT3512
F: Uncharacterized protein Rv3404c/MT3512
G: Uncharacterized protein Rv3404c/MT3512
H: Uncharacterized protein Rv3404c/MT3512
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,88330
Polymers231,5188
Non-polymers1,36522
Water17,529973
1
A: Uncharacterized protein Rv3404c/MT3512
B: Uncharacterized protein Rv3404c/MT3512
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2528
Polymers57,8792
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-2 kcal/mol
Surface area21670 Å2
MethodPISA
2
C: Uncharacterized protein Rv3404c/MT3512
D: Uncharacterized protein Rv3404c/MT3512
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3149
Polymers57,8792
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint6 kcal/mol
Surface area22220 Å2
MethodPISA
3
E: Uncharacterized protein Rv3404c/MT3512
F: Uncharacterized protein Rv3404c/MT3512
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2528
Polymers57,8792
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-1 kcal/mol
Surface area21510 Å2
MethodPISA
4
G: Uncharacterized protein Rv3404c/MT3512
H: Uncharacterized protein Rv3404c/MT3512
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0665
Polymers57,8792
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-12 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.080, 136.450, 99.970
Angle α, β, γ (deg.)90.000, 103.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA1 - 23122 - 252
21LYSLYSBB1 - 23122 - 252
12ALAALAAA1 - 23522 - 256
22ALAALACC1 - 23522 - 256
13ALAALAAA1 - 23522 - 256
23ALAALADD1 - 23522 - 256
14LYSLYSAA1 - 23122 - 252
24LYSLYSEE1 - 23122 - 252
15ALAALAAA1 - 23522 - 256
25ALAALAFF1 - 23522 - 256
16LYSLYSAA1 - 23122 - 252
26LYSLYSGG1 - 23122 - 252
17GLUGLUAA1 - 23022 - 251
27GLUGLUHH1 - 23022 - 251
18LYSLYSBB1 - 23122 - 252
28LYSLYSCC1 - 23122 - 252
19LYSLYSBB1 - 23122 - 252
29LYSLYSDD1 - 23122 - 252
110PROPROBB1 - 23222 - 253
210PROPROEE1 - 23222 - 253
111LYSLYSBB1 - 23122 - 252
211LYSLYSFF1 - 23122 - 252
112PROPROBB1 - 23222 - 253
212PROPROGG1 - 23222 - 253
113GLUGLUBB1 - 23022 - 251
213GLUGLUHH1 - 23022 - 251
114ALAALACC1 - 23522 - 256
214ALAALADD1 - 23522 - 256
115LYSLYSCC1 - 23122 - 252
215LYSLYSEE1 - 23122 - 252
116ALAALACC1 - 23522 - 256
216ALAALAFF1 - 23522 - 256
117LYSLYSCC1 - 23122 - 252
217LYSLYSGG1 - 23122 - 252
118GLUGLUCC1 - 23022 - 251
218GLUGLUHH1 - 23022 - 251
119LYSLYSDD1 - 23122 - 252
219LYSLYSEE1 - 23122 - 252
120ALAALADD1 - 23522 - 256
220ALAALAFF1 - 23522 - 256
121LYSLYSDD1 - 23122 - 252
221LYSLYSGG1 - 23122 - 252
122GLUGLUDD1 - 23022 - 251
222GLUGLUHH1 - 23022 - 251
123LYSLYSEE1 - 23122 - 252
223LYSLYSFF1 - 23122 - 252
124PROPROEE1 - 23222 - 253
224PROPROGG1 - 23222 - 253
125GLUGLUEE1 - 23022 - 251
225GLUGLUHH1 - 23022 - 251
126LYSLYSFF1 - 23122 - 252
226LYSLYSGG1 - 23122 - 252
127GLUGLUFF1 - 23022 - 251
227GLUGLUHH1 - 23022 - 251
128GLUGLUGG1 - 23022 - 251
228GLUGLUHH1 - 23022 - 251

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Uncharacterized protein Rv3404c/MT3512


Mass: 28939.691 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT3412, MT3512, MTCY78.24, Rv3404c / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: P65073, UniProt: P9WKZ3*PLUS
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / 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: 51.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MytuD.17389.a.A1.PW30616 at 19 mg/mL against JCSG+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 supplemented with 25% ethylene glycol, crystal tracking ID 220349d6, ...Details: MytuD.17389.a.A1.PW30616 at 19 mg/mL against JCSG+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 supplemented with 25% ethylene glycol, crystal tracking ID 220349d6, unique puck ID bdu3-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 128170 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.095 Å2 / Rmerge(I) obs: 0.06 / Χ2: 0.959 / Net I/σ(I): 15.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.4622.9734759932599.9
2.21-2.270.3973.5233748901799.8
2.27-2.330.3264.2433082876799.9
2.33-2.40.2685.0932578856599.9
2.4-2.480.2216.1631582827799.8
2.48-2.570.1777.4930435799099.9
2.57-2.670.1488.9729594772999.8
2.67-2.780.1210.7228569746399.8
2.78-2.90.09413.1727184710299.9
2.9-3.040.0831526229685699.8
3.04-3.210.06518.1924729649999.9
3.21-3.40.05123.0123304613199.8
3.4-3.630.04227.1121799575499.8
3.63-3.930.03630.9520465541199.9
3.93-4.30.03433.6618867497399.8
4.3-4.810.0335.4117032447099.8
4.81-5.550.0335.2415213398199.8
5.55-6.80.0334.1112848336899.8
6.8-9.620.02737.799860260799.9
9.620.02638.164941141996.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NV1

4nv1


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2236 / WRfactor Rwork: 0.1817 / FOM work R set: 0.8244 / SU B: 10.325 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1956 / SU Rfree: 0.1728 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.231 6535 4.9 %RANDOM
Rwork0.1867 ---
obs0.1889 128170 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.97 Å2 / Biso mean: 40.346 Å2 / Biso min: 20.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.3 Å2
2---0.25 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14616 0 88 973 15677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915058
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.94120461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74151867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96323.333774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.906152295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.10115138
X-RAY DIFFRACTIONr_chiral_restr0.0920.22262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111802
X-RAY DIFFRACTIONr_mcbond_it1.3112.1267468
X-RAY DIFFRACTIONr_mcangle_it2.0123.1799323
X-RAY DIFFRACTIONr_scbond_it1.9622.3417590
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3010.03
12B3010.03
21A3000.03
22C3000.03
31A3070.08
32D3070.08
41A3000.03
42E3000.03
51A3020.03
52F3020.03
61A3000.04
62G3000.04
71A2980.03
72H2980.03
81B2970.01
82C2970.01
91B2980.06
92D2980.06
101B3020.02
102E3020.02
111B2960.01
112F2960.01
121B3000.04
122G3000.04
131B2960.01
132H2960.01
141C3040.06
142D3040.06
151C2990.02
152E2990.02
161C3010.01
162F3010.01
171C2970.04
172G2970.04
181C2970.01
182H2970.01
191D2990.05
192E2990.05
201D3040.07
202F3040.07
211D3010.07
212G3010.07
221D2980.05
222H2980.05
231E2980.01
232F2980.01
241E3030.04
242G3030.04
251E2990.01
252H2990.01
261F2970.04
262G2970.04
271F2950.01
272H2950.01
281G2950.04
282H2950.04
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 488 -
Rwork0.256 9347 -
all-9835 -
obs--99.85 %
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)
10.8626-0.2363-0.32062.0439-0.72990.79850.04810.02810.1736-0.02410.06420.16230.0244-0.0703-0.11230.0177-0.0025-0.00960.1073-0.02620.1234-6.37250.7346-35.6342
20.9872-0.56390.76280.8152-0.31270.8362-0.0087-0.0581-0.08150.04580.03070.0310.0503-0.0232-0.0220.0976-0.01080.00250.11080.0310.047716.2407-35.6016-12.5653
31.3595-0.77230.58051.9981-0.29070.8401-0.01510.05320.0991-0.1618-0.0405-0.0127-0.0308-0.07440.05560.081-0.01840.02860.107-0.01510.033822.8564-4.0011-59.4349
40.9366-0.27640.58121.5969-0.79661.8224-0.0444-0.0191-0.10880.1632-0.0298-0.35340.03880.07060.07420.03360.0133-0.02730.0937-0.01580.16849.9929-30.3826-29.3541
50.8432-0.66061.05210.9217-0.75951.7386-0.01860.06090.1027-0.0889-0.1034-0.2140.0040.08930.1220.03420.01250.0130.11840.04190.198740.888324.1721-41.8847
61.1221-0.08190.71731.3548-0.44132.31680.1405-0.1398-0.03140.2474-0.045-0.20870.3104-0.0081-0.09550.1717-0.0072-0.15260.1304-0.0050.176757.6513-2.182-4.7861
70.553-0.34190.37364.3018-1.59881.22070.00880.03530.06740.7994-0.1176-0.0605-0.32460.00790.10880.172-0.02640.00350.0565-0.01350.057211.328529.2648-18.2834
81.4683-1.24560.74093.653-2.10421.5507-0.25730.0345-0.01941.18050.0199-0.0878-0.64820.15380.23740.6965-0.0908-0.02580.33040.0050.136923.2306-7.936212.1134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 235
2X-RAY DIFFRACTION2B1 - 232
3X-RAY DIFFRACTION3C1 - 235
4X-RAY DIFFRACTION4D1 - 235
5X-RAY DIFFRACTION5E1 - 232
6X-RAY DIFFRACTION6F1 - 235
7X-RAY DIFFRACTION7G1 - 232
8X-RAY DIFFRACTION8H1 - 231

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