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- PDB-7mj0: LarB, a carboxylase/hydrolase involved in synthesis of the cofact... -

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Basic information

Entry
Database: PDB / ID: 7mj0
TitleLarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP
ComponentsPyridinium-3,5-biscarboxylic acid mononucleotide synthase
KeywordsLYASE (CARBON-CARBON) / Carboxylase / Hydrolase
Function / homology
Function and homology information


pyridinium-3,5-biscarboxylic acid mononucleotide synthase / 'de novo' IMP biosynthetic process / transferase activity / hydrolase activity / plasma membrane
Similarity search - Function
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / PurE domain / AIR carboxylase / AIR carboxylase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsChatterjee, S. / Rankin, J.A. / Lagishetty, S. / Hu, J. / Hausinger, R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1807073 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis.
Authors: Rankin, J.A. / Chatterjee, S. / Tariq, Z. / Lagishetty, S. / Desguin, B. / Hu, J. / Hausinger, R.P.
History
DepositionApr 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,80410
Polymers159,0616
Non-polymers7434
Water0
1
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,66520
Polymers212,0828
Non-polymers1,58312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area23800 Å2
ΔGint-273 kcal/mol
Surface area53780 Å2
MethodPISA
2
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,47112
Polymers212,0828
Non-polymers1,3894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area22310 Å2
ΔGint-186 kcal/mol
Surface area56110 Å2
MethodPISA
3
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase


Theoretical massNumber of molelcules
Total (without water)212,0828
Polymers212,0828
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area19220 Å2
ΔGint-161 kcal/mol
Surface area54670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.284, 121.284, 213.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB ...P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB / Lactate racemase maturation protein LarB / Lactate racemization operon protein LarB / Nickel-pincer cofactor biosynthesis protein LarB / Nicotinic acid adenine dinucleotide carboxylase/hydrolase / NaAD carboxylase/hydrolase


Mass: 26510.227 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larB, lp_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F9UST0, pyridinium-3,5-biscarboxylic acid mononucleotide synthase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 100 mM Magnesium formate, 2 mM nitrilotriacetic acid (pH to 7.5 with sodium hydroxide), 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM AMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.01→40 Å / Num. obs: 32347 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.049 / Rrim(I) all: 0.153 / Χ2: 0.84 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.09-3.219.60.98828920.7870.3340.666100
3.21-3.349.90.68429330.9080.2280.7031000.722
3.34-3.499.90.46829130.960.1560.7761000.494
3.49-3.689.90.39829420.9650.1320.821000.42
3.68-3.919.90.25429170.9840.0840.8731000.268
3.91-4.219.90.16829450.9940.0560.8251000.177
4.21-4.639.80.10929720.9960.0360.8921000.115
4.63-5.39.70.10129850.9970.0341.061000.106
5.3-6.679.60.10130360.9960.0340.9721000.107
3.01-3.179.146190.69999.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D7A

1d7a


Resolution: 3.01→39.788 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 1673 5.18 %
Rwork0.2353 30647 -
obs0.2373 32320 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 309.75 Å2 / Biso mean: 108.5008 Å2 / Biso min: 22.89 Å2
Refinement stepCycle: final / Resolution: 3.01→39.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8501 0 48 0 8549
Biso mean--67.09 --
Num. residues----1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018679
X-RAY DIFFRACTIONf_angle_d1.1511875
X-RAY DIFFRACTIONf_dihedral_angle_d14.0912946
X-RAY DIFFRACTIONf_chiral_restr0.2071494
X-RAY DIFFRACTIONf_plane_restr0.0081528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0103-3.09890.36081570.33562474100
3.0989-3.19890.34881250.31812525100
3.1989-3.31310.31781420.29812498100
3.3131-3.44570.32041240.2732511100
3.4457-3.60240.34781320.25932520100
3.6024-3.79220.29231410.25942529100
3.7922-4.02960.27261350.23762531100
4.0296-4.34040.23471570.21042526100
4.3404-4.77650.2221490.17962544100
4.7765-5.46620.21651150.21362616100
5.4662-6.8810.32721590.26242599100
6.881-39.7880.25161370.2075277499
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)
16.7583-3.32093.64063.89162.29459.3830.336-0.4101-0.14870.32610.1989-0.34070.20730.3014-0.27511.3509-0.24510.50810.7508-0.26340.73645.0561-23.46595.6437
23.6406-0.09911.39925.5981.64131.9732-0.14441.283-0.9939-1.1553-0.3548-0.73520.06540.13830.27131.6079-0.08780.5981.0359-0.21230.91744.0468-19.2053-4.3853
35.1599-1.5094-3.49582.4974-0.75964.5112-0.76591.1293-0.9766-1.2359-0.14480.59531.3414-0.51620.86340.7131-0.1862-0.06220.8186-0.36640.744928.6997-14.63958.3992
43.2022-0.526-0.16544.07160.61914.4015-0.05630.31960.4255-0.3663-0.15780.289-0.1443-0.19890.1320.27780.0065-0.07320.2625-0.0470.425736.0665-5.673615.4687
54.0217-1.9321-0.03963.19111.2836.42040.3924-1.32681.60760.9645-0.20630.7091-0.45160.03650.40740.8457-0.26430.29231.1744-0.9491.052430.4109-6.287344.8182
62.1631.28820.24092.1837-0.15272.4412-0.1454-2.0318-0.29450.6948-0.30680.02550.12120.46660.29510.5387-0.01270.03570.94240.03240.462139.5708-20.245340.8482
77.291-0.0376-1.56424.48260.41254.6701-0.1292-0.4008-0.00860.0006-0.1091-0.4664-0.02290.50770.22640.2425-0.03420.02320.37130.05280.358945.0959-18.052426.9497
87.1866-3.4967-2.97273.3019-1.03335.12860.0585-0.33720.2546-0.48330.07151.15490.2624-0.47940.19940.81350.1689-0.3720.69080.06271.0159-1.7895-31.911326.6353
93.0007-0.5249-0.49060.09740.01390.93410.2327-0.12210.5632-0.09270.33960.1731-0.0834-0.1932-0.36321.23480.2006-0.65751.5699-0.10251.3278-5.0973-30.82117.8307
102.9781-0.11630.70870.08310.69156.4761-0.05641.4524-0.2307-1.44510.21350.3611.19280.106-0.42741.82760.2059-0.53191.2570.05140.69762.4469-37.151215.2405
113.30261.23621.4954.45471.81974.2504-0.06930.43310.4768-2.0981-0.14140.4416-0.8437-0.43210.38190.95360.0821-0.04030.53090.01930.495712.8681-32.704125.2331
123.31250.41040.29753.63950.5122.75330.05910.0704-0.3584-0.5581-0.2412-0.7049-0.06950.27580.30380.355-0.00520.07290.35980.10610.456919.8811-39.545335.369
132.7875-0.0531-0.75365.5249-0.61483.77840.114-0.1176-0.43530.1266-0.29030.30910.05020.12980.17890.2065-0.06260.04830.37560.05820.333810.4953-41.368739.3023
143.0996-1.39591.41522.10050.31925.78860.1249-0.4812-0.2489-0.22440.4489-0.97690.856-0.3775-0.36821.3212-0.4635-0.41830.75450.48851.374820.7816-37.165360.3419
152.2532-1.2496-1.23762.8538-1.59113.06730.4098-1.4417-0.80151.1858-0.1258-1.00430.23080.6049-0.04141.0015-0.4405-0.61471.69420.1790.746220.2271-37.374868.2952
162.7257-0.338-0.65244.3556-4.05584.8880.1077-0.98510.22451.3394-0.4434-0.45250.00640.01780.30541.6523-1.0073-0.36872.6370.39581.008714.2105-38.292877.4106
171.712-1.95682.15092.8395-2.02184.790.6293-1.79890.37111.257-1.25790.2976-0.175-0.52990.45780.719-0.40390.02271.4061-0.24910.64746.4702-31.404661.6654
183.28481.05483.01681.37460.3193.18180.045-1.77411.13870.6541-0.61041.3003-0.5932-0.71570.33250.5001-0.14830.06750.9414-0.54081.0798-4.6959-27.457253.0851
194.4697-1.39781.52595.7194-0.52637.67630.237-1.03730.23140.423-0.07290.81190.3228-0.7039-0.14110.4353-0.08710.08070.5835-0.1550.4522-1.8886-36.36548.5587
204.79752.02930.98414.21.16557.81880.4844-1.068-0.60290.4018-0.6601-0.45550.63420.09640.2040.3966-0.0704-0.01660.53720.02060.41955.2313-39.571748.1299
213.67041.4114-0.35662.6165-1.10082.47530.2639-0.0501-0.113-1.095-1.18370.30810.27780.0340.58682.50090.4981.03122.10870.06741.480260.25-25.918170.0246
222.6546-1.4141-1.95744.52183.38493.0247-0.51830.2075-1.1058-0.1485-0.77090.55471.5929-0.21921.12572.5343-0.5011.0891.8864-0.86371.520843.8487-29.725780.8797
231.76790.75280.08971.6564-0.15162.56050.145-0.2734-0.1391-0.7627-0.56410.48280.3962-0.73810.47012.1782-0.54940.81992.3955-1.21251.243239.7266-21.599283.1555
244.8284-0.5521-3.57770.3003-0.54136.42170.13310.6592-0.0103-0.17860.0569-0.0819-0.0348-0.9248-0.02381.731-0.58321.49531.8884-0.98991.462841.8828-18.347690.7648
252.8852-2.0605-1.64061.9542.42074.1452-0.3274-0.2532-0.45080.3183-0.06660.48450.56990.26150.21291.9633-0.60060.99441.7662-0.90331.526745.1005-15.732490.9399
261.4889-1.4847-0.6016.35773.65792.7217-0.3434-0.13320.1699-0.2714-0.55860.27571.04640.26010.26511.8742-0.39691.23611.4305-0.44431.576851.0743-19.245191.4767
270.8579-0.30121.39944.43014.14547.29780.2221-1.06840.27810.0729-0.52170.41930.4973-0.74740.01592.2195-0.57990.97962.1053-0.30061.578140.982-21.2815117.9114
286.283-2.7138-6.33882.47942.0269.4907-0.1736-0.7654-0.7722-0.4995-0.953-0.51361.3509-1.26740.97552.3086-0.26510.98481.87020.1731.605549.9842-28.172117.9628
295.6984-1.7307-0.59882.4782-2.89638.3349-1.24521.6426-0.7501-0.4760.7288-0.27590.5341-0.25240.40522.6256-0.10191.38851.93320.32221.328156.8603-25.3797112.1913
300.3014-0.2893-0.02620.96060.25162.19-0.2486-0.4759-0.3040.406-0.8795-0.12021.3337-0.15150.0692.9233-0.13542.31931.12110.78791.660260.3864-25.5608101.1533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 58 )A44 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 107 )A59 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 125 )A108 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 246 )A126 - 246
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 82 )B44 - 82
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 162 )B83 - 162
7X-RAY DIFFRACTION7chain 'B' and (resid 163 through 246 )B163 - 246
8X-RAY DIFFRACTION8chain 'C' and (resid 44 through 58 )C44 - 58
9X-RAY DIFFRACTION9chain 'C' and (resid 59 through 74 )C59 - 74
10X-RAY DIFFRACTION10chain 'C' and (resid 75 through 96 )C75 - 96
11X-RAY DIFFRACTION11chain 'C' and (resid 97 through 125 )C97 - 125
12X-RAY DIFFRACTION12chain 'C' and (resid 126 through 199 )C126 - 199
13X-RAY DIFFRACTION13chain 'C' and (resid 200 through 250 )C200 - 250
14X-RAY DIFFRACTION14chain 'D' and (resid 43 through 58 )D43 - 58
15X-RAY DIFFRACTION15chain 'D' and (resid 59 through 82 )D59 - 82
16X-RAY DIFFRACTION16chain 'D' and (resid 83 through 96 )D83 - 96
17X-RAY DIFFRACTION17chain 'D' and (resid 97 through 141 )D97 - 141
18X-RAY DIFFRACTION18chain 'D' and (resid 142 through 169 )D142 - 169
19X-RAY DIFFRACTION19chain 'D' and (resid 170 through 207 )D170 - 207
20X-RAY DIFFRACTION20chain 'D' and (resid 208 through 246 )D208 - 246
21X-RAY DIFFRACTION21chain 'E' and (resid 49 through 107 )E49 - 107
22X-RAY DIFFRACTION22chain 'E' and (resid 108 through 126 )E108 - 126
23X-RAY DIFFRACTION23chain 'E' and (resid 127 through 168 )E127 - 168
24X-RAY DIFFRACTION24chain 'E' and (resid 169 through 188 )E169 - 188
25X-RAY DIFFRACTION25chain 'E' and (resid 189 through 207 )E189 - 207
26X-RAY DIFFRACTION26chain 'E' and (resid 208 through 246 )E208 - 246
27X-RAY DIFFRACTION27chain 'F' and (resid 46 through 85 )F46 - 85
28X-RAY DIFFRACTION28chain 'F' and (resid 86 through 125 )F86 - 125
29X-RAY DIFFRACTION29chain 'F' and (resid 126 through 141 )F126 - 141
30X-RAY DIFFRACTION30chain 'F' and (resid 142 through 246 )F142 - 246

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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