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- PDB-3lp6: Crystal Structure of Rv3275c-E60A from Mycobacterium tuberculosis... -

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Basic information

Entry
Database: PDB / ID: 3lp6
TitleCrystal Structure of Rv3275c-E60A from Mycobacterium tuberculosis at 1.7A resolution
ComponentsPhosphoribosylaminoimidazole carboxylase catalytic subunit
KeywordsLYASE / alpha and beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / TB Structural Genomics Consortium / TBSGC / Decarboxylase / Purine biosynthesis
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
: / Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / N5-carboxyaminoimidazole ribonucleotide mutase / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsKim, H. / Yu, M. / Hung, L.-W. / Terwilliger, T.C. / Kim, C.-Y. / Integrated Center for Structure and Function Innovation (ISFI) / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of Rv3275c-E60A from Mycobacterium tuberculosis at 1.7A Resolution
Authors: Kim, H. / Yu, M. / Hung, L.-W. / Terwilliger, T.C. / Kim, C.-Y.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
B: Phosphoribosylaminoimidazole carboxylase catalytic subunit
C: Phosphoribosylaminoimidazole carboxylase catalytic subunit
D: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,73128
Polymers70,5344
Non-polymers1,19724
Water7,350408
1
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
B: Phosphoribosylaminoimidazole carboxylase catalytic subunit
C: Phosphoribosylaminoimidazole carboxylase catalytic subunit
D: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules

A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
B: Phosphoribosylaminoimidazole carboxylase catalytic subunit
C: Phosphoribosylaminoimidazole carboxylase catalytic subunit
D: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,46156
Polymers141,0688
Non-polymers2,39348
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area42310 Å2
ΔGint-239 kcal/mol
Surface area38530 Å2
MethodPISA
2
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
B: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules

C: Phosphoribosylaminoimidazole carboxylase catalytic subunit
D: Phosphoribosylaminoimidazole carboxylase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,73128
Polymers70,5344
Non-polymers1,19724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9760 Å2
ΔGint-47 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.696, 145.696, 58.384
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
Phosphoribosylaminoimidazole carboxylase catalytic subunit / AIR carboxylase / AIRC


Mass: 17633.453 Da / Num. of mol.: 4 / Mutation: E60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: MT3375, MTCY71.15c, purE, Rv3275c / Plasmid: Custom / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96880, UniProt: P9WHM1*PLUS, phosphoribosylaminoimidazole carboxylase
#2: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1M Na acetate pH5.4, 1.7M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 69300 / Num. obs: 63825 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6825 / % possible all: 85

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_292)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O4VA

Resolution: 1.702→45.558 Å / SU ML: 0.16 / σ(F): 1.33 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 2029 3.22 %RANDOM
Rwork0.1682 ---
obs0.1693 62961 90.97 %-
all-68915 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.668 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.7572 Å2-0 Å20 Å2
2---5.7572 Å20 Å2
3---11.5143 Å2
Refinement stepCycle: LAST / Resolution: 1.702→45.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4737 0 78 408 5223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064934
X-RAY DIFFRACTIONf_angle_d0.9936694
X-RAY DIFFRACTIONf_dihedral_angle_d13.0581784
X-RAY DIFFRACTIONf_chiral_restr0.064794
X-RAY DIFFRACTIONf_plane_restr0.004890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.702-1.76280.25221860.19625591X-RAY DIFFRACTION85
1.7628-1.83340.23551860.18155573X-RAY DIFFRACTION84
1.8334-1.91690.22121900.17625696X-RAY DIFFRACTION86
1.9169-2.01790.24942050.18016067X-RAY DIFFRACTION92
2.0179-2.14440.24032000.16896099X-RAY DIFFRACTION92
2.1444-2.30990.19742000.1676134X-RAY DIFFRACTION92
2.3099-2.54240.20832080.17346112X-RAY DIFFRACTION92
2.5424-2.91020.25462080.17796271X-RAY DIFFRACTION93
2.9102-3.66630.1642160.1576434X-RAY DIFFRACTION95
3.6663-45.57430.17032300.15656955X-RAY DIFFRACTION98
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)
10.15280.37450.03391.46720.48150.2929-0.1160.2331-0.1716-0.42940.1815-0.0924-0.03450.0585-0.04140.2319-0.0112-0.00670.1948-0.0410.219956.285919.863713.5725
21.08350.0706-0.01280.3882-0.02640.06440.07490.1749-0.2777-0.26580.0235-0.1075-0.00950.0132-0.05380.2304-0.00840.0320.2174-0.10920.21256.599817.002815.2091
30.7407-0.50560.21140.50860.01430.5571-0.0173-0.1257-0.0424-0.11350.11420.01390.1603-0.0096-0.10030.1542-0.0028-0.04260.1352-0.02880.287251.22099.718722.5192
40.7811-0.12850.1310.32040.2310.29390.0209-0.0032-0.0889-0.0790.01560.0533-0.0246-0.0277-0.03070.11880.0021-0.00310.1412-0.01560.1551.736925.38724.7943
50.10880.4556-0.15932.4549-0.61760.31-0.20910.0358-0.131-0.22940.1725-0.73810.1855-0.02020.03030.16350.01810.04110.2057-0.06720.324273.992323.046420.9916
62.8896-2.69840.12843.4414-0.26750.0980.03910.6106-0.1146-0.201-0.24070.0913-0.0505-0.01960.1730.2146-0.0060.03910.2778-0.03610.250971.423544.59948.871
71.36840.0298-0.29030.2488-0.23710.34640.22320.28950.0847-0.2314-0.0683-0.0171-0.0132-0.0007-0.10560.2219-0.00270.05780.19490.01110.195264.848256.177713.979
81.6979-2.3465-0.03913.57790.30680.19270.10020.23920.5159-0.4786-0.0192-0.7116-0.1233-0.0644-0.07570.2257-0.01690.10940.19030.04480.325468.456160.681414.551
90.2540.0459-0.2840.59790.05010.41180.1267-0.02980.04660.0217-0.0907-0.2041-0.00820.0524-0.03880.1528-0.00760.0420.1834-0.03710.317374.488149.468122.9868
100.195-0.2117-0.12030.25850.12980.3860.02130.06370.0427-0.07690.02-0.07340.0418-0.0151-0.03960.1456-0.01350.01650.1273-0.00710.178259.988251.916625.271
111.1332-0.75210.05710.598-0.14670.12080.05910.09330.66160.1869-0.1535-0.5342-0.14430.12310.09530.2448-0.02040.00690.1470.06310.414260.6274.48321.2426
121.03661.4580.04882.14620.02910.0894-0.00720.33970.3212-0.14060.00430.45080.2708-0.0585-0.01830.26530.0046-0.00290.25040.10330.347435.164973.09948.4001
130.8106-0.39880.82450.9736-0.76711.05330.0671-0.2883-0.04470.32260.0252-0.21350.0194-0.0479-0.05360.16710.0037-0.04840.20580.01320.181766.886328.353643.4071
140.2284-0.0896-0.08960.56860.0130.0817-0.0495-0.2933-0.14130.25250.0709-0.20280.0456-0.0318-0.01350.19220.0215-0.07510.20250.03760.252368.973223.448742.8385
150.23670.26580.16181.1173-0.00930.45920.03480.0050.01890.0464-0.0595-0.2947-0.03410.18240.01760.13340.0037-0.01330.1787-0.02530.313574.63835.997933.9202
160.42560.01750.23650.51880.08010.21-0.0112-0.10390.00120.03360.0329-0.0428-0.07610.0038-0.01780.11850.004-0.00110.1293-0.00990.131560.130333.487532.2737
170.81820.11260.02480.11290.12720.24110.1679-0.2069-0.39910.0512-0.0977-0.15210.05610.157-0.04510.17680.0298-0.02540.1710.04930.305661.438910.680335.9582
180.372-0.2153-0.5511.01440.20771.08190.0476-0.0679-0.09260.3102-0.12780.3367-0.1784-0.30020.03040.25790.02240.04520.26990.1110.32636.37912.088449.3532
190.2641-0.53190.07771.2472-0.46240.548-0.1232-0.1758-0.10680.27030.24770.3912-0.065-0.1095-0.10680.19320.00150.03140.20560.0930.259528.714716.925244.4044
202.8002-0.58810.10570.2821-0.14761.1112-0.0642-0.307-0.52790.22860.19930.3688-0.1371-0.151-0.03130.19140.00850.05890.21250.13590.257323.923618.266544.037
210.4953-0.47980.40040.9775-0.8980.8353-0.0040.0695-0.2372-0.18370.02130.08360.19470.0265-0.02140.1556-0.0022-0.02760.12010.03730.304936.720711.021434.2092
220.2527-0.32790.12260.4573-0.26460.37060.0277-0.0059-0.1257-0.04180.0410.030.00080.0397-0.06080.1168-0.0133-0.01530.13820.02460.168333.669925.170132.6302
230.0477-0.03160.01880.9082-0.19860.0776-0.2433-0.0526-0.30850.06790.37520.780.2719-0.0091-0.14320.1407-0.05140.02060.22150.15850.536911.326121.988536.2399
243.27151.2219-0.70590.811-0.35110.21030.0643-0.76180.09710.2266-0.14750.22680.18150.1340.05860.2322-0.04460.04930.35550.02220.275313.627442.827348.635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:31)A6 - 31
2X-RAY DIFFRACTION2(chain A and resid 32:45)A32 - 45
3X-RAY DIFFRACTION3(chain A and resid 46:64)A46 - 64
4X-RAY DIFFRACTION4(chain A and resid 65:133)A65 - 133
5X-RAY DIFFRACTION5(chain A and resid 134:150)A134 - 150
6X-RAY DIFFRACTION6(chain A and resid 151:169)A151 - 169
7X-RAY DIFFRACTION7(chain B and resid 7:31)B7 - 31
8X-RAY DIFFRACTION8(chain B and resid 32:42)B32 - 42
9X-RAY DIFFRACTION9(chain B and resid 43:64)B43 - 64
10X-RAY DIFFRACTION10(chain B and resid 65:133)B65 - 133
11X-RAY DIFFRACTION11(chain B and resid 134:153)B134 - 153
12X-RAY DIFFRACTION12(chain B and resid 154:173)B154 - 173
13X-RAY DIFFRACTION13(chain C and resid 4:31)C4 - 31
14X-RAY DIFFRACTION14(chain C and resid 32:41)C32 - 41
15X-RAY DIFFRACTION15(chain C and resid 42:64)C42 - 64
16X-RAY DIFFRACTION16(chain C and resid 65:133)C65 - 133
17X-RAY DIFFRACTION17(chain C and resid 134:152)C134 - 152
18X-RAY DIFFRACTION18(chain C and resid 153:173)C153 - 173
19X-RAY DIFFRACTION19(chain D and resid 1:24)D1 - 24
20X-RAY DIFFRACTION20(chain D and resid 25:41)D25 - 41
21X-RAY DIFFRACTION21(chain D and resid 42:64)D42 - 64
22X-RAY DIFFRACTION22(chain D and resid 65:133)D65 - 133
23X-RAY DIFFRACTION23(chain D and resid 134:149)D134 - 149
24X-RAY DIFFRACTION24(chain D and resid 150:168)D150 - 168

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