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- PDB-5far: Crystal structure of dihydroneopterin aldolase from Bacillus anth... -

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Basic information

Entry
Database: PDB / ID: 5far
TitleCrystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with 9-METHYLGUANINE
Components7,8-dihydroneopterin aldolase
KeywordsLYASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / dihydroneopterin aldolase / Bacillus anthracis
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
9-METHYLGUANINE / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesBacillus cereus BAG3X2-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with 9-METHYLGUANINE
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_reflns_twin / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
E: 7,8-dihydroneopterin aldolase
F: 7,8-dihydroneopterin aldolase
G: 7,8-dihydroneopterin aldolase
H: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,20916
Polymers114,8888
Non-polymers1,3218
Water2,468137
1
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1048
Polymers57,4444
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-18 kcal/mol
Surface area21580 Å2
MethodPISA
2
E: 7,8-dihydroneopterin aldolase
F: 7,8-dihydroneopterin aldolase
G: 7,8-dihydroneopterin aldolase
H: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1048
Polymers57,4444
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-18 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.795, 138.209, 63.933
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
7,8-dihydroneopterin aldolase


Mass: 14360.960 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus BAG3X2-1 (bacteria) / Gene: IE3_00005 / Plasmid: pMCSG28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: J7VEZ6, dihydroneopterin aldolase
#2: Chemical
ChemComp-9MG / 9-METHYLGUANINE


Mass: 165.153 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H7N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium acetate, 0.1M Bis-Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.538
11h,-k,-l20.096
11L, -K, H30.281
11-L, K, H40.085
ReflectionResolution: 2→45.21 Å / Num. obs: 62246 / % possible obs: 84.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.055 / Rrim(I) all: 0.124 / Χ2: 0.907 / Net I/av σ(I): 11.793 / Net I/σ(I): 7.5 / Num. measured all: 288910
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.58524430.760.3030.6620.8667.1
2.03-2.0740.56625770.7590.290.6390.84171.1
2.07-2.114.10.56726770.8240.2860.6370.87172.7
2.11-2.154.20.48228540.8750.2430.5420.86777.6
2.15-2.24.30.42529960.8860.2140.4780.85381.1
2.2-2.254.40.40430620.8930.2030.4540.85483.9
2.25-2.314.60.37231920.9420.1850.4170.86787
2.31-2.374.70.33632270.950.1670.3770.86487.7
2.37-2.444.90.35132010.9370.1730.3920.85287.3
2.44-2.524.90.31231910.9420.1530.3490.85887.6
2.52-2.614.90.2431770.9620.1180.2680.87187
2.61-2.714.90.20431790.9650.1010.2280.89486.2
2.71-2.844.80.16831590.9730.0830.1880.89686
2.84-2.994.80.14431570.9760.0720.1620.92885.7
2.99-3.174.80.12231270.9790.0610.1371.01485
3.17-3.424.70.10631370.980.0530.1191.06485.6
3.42-3.764.60.09831790.980.050.1111.1385.7
3.76-4.314.50.08533670.9840.0430.0961.01291.2
4.31-5.434.80.07736250.9830.0380.0870.85798.2
5.43-505.50.08437190.9860.040.0930.8699.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NM2
Resolution: 2→45.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.865 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23253 3024 4.8 %RANDOM
Rwork0.19312 ---
obs0.19494 59338 83.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.535 Å2
Baniso -1Baniso -2Baniso -3
1--40.64 Å2-0 Å2-5.05 Å2
2--89.11 Å20 Å2
3----48.48 Å2
Refinement stepCycle: LAST / Resolution: 2→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7831 0 96 137 8064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198218
X-RAY DIFFRACTIONr_bond_other_d0.0020.027811
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.99611120
X-RAY DIFFRACTIONr_angle_other_deg0.93318033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3795973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00523.957417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.105151454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1111566
X-RAY DIFFRACTIONr_chiral_restr0.0830.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219171
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021827
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7282.1483880
X-RAY DIFFRACTIONr_mcbond_other0.7282.1473879
X-RAY DIFFRACTIONr_mcangle_it1.2963.2174857
X-RAY DIFFRACTIONr_mcangle_other1.2963.2184858
X-RAY DIFFRACTIONr_scbond_it0.5862.2494338
X-RAY DIFFRACTIONr_scbond_other0.5862.2494339
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9453.3556264
X-RAY DIFFRACTIONr_long_range_B_refined5.05717.9399084
X-RAY DIFFRACTIONr_long_range_B_other5.04217.8669058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 172 -
Rwork0.289 3111 -
obs--59.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0965-0.16940.08521.2071.47653.0478-0.0107-0.10890.0017-0.05680.08090.001-0.2943-0.3653-0.07020.33170.15210.01250.19490.06490.3678-0.598392.3374-10.951
20.4729-1.145-0.14775.8473-4.13536.6549-0.0392-0.0565-0.1740.6546-0.30240.1721-0.91460.64480.34160.46840.0941-0.00220.2413-0.10120.4021-4.5428107.818411.4669
30.12790.0773-0.55261.39612.47238.5949-0.00860.05530.1893-0.1760.0550.4221-0.4531-0.3428-0.04640.27380.253-0.06370.29220.06850.4028-8.047197.7084-6.3906
41.2372-0.4734-2.02550.18450.74343.87470.10360.2430.2024-0.0518-0.1137-0.0893-0.2649-0.23690.01010.39870.2304-0.02390.24520.14410.3335-5.691106.4945-6.1771
51.9542-2.5333-1.02433.92031.73781.6233-0.02240.08490.18930.07480.15-0.0659-0.2117-0.0627-0.12760.37310.07660.01840.15530.08190.35316.097497.0319-12.606
61.8706-1.17020.20481.02920.06810.23010.07690.17050.0655-0.1-0.0844-0.0283-0.210.08240.00750.4634-0.07580.01330.13480.03210.311426.421592.3405-14.9711
72.0147-0.94030.17012.67730.57870.985-0.1006-0.1220.2992-0.22050.10440.0318-0.6960.0675-0.00380.63020.00530.00960.07090.05780.30518.3818103.4422-17.9694
87.3701-2.0234-0.29060.55660.0681.67810.12810.10280.0231-0.0457-0.01860.0031-0.2335-0.111-0.10950.4069-0.0146-0.01290.09020.06160.346916.087196.9326-23.4526
91.6407-1.42490.05123.4396-2.02451.8080.21890.2446-0.04110.266-0.24040.0396-0.52260.07510.02150.7146-0.1491-0.03530.09720.05780.340324.3754103.4699-20.5724
100.304-0.75870.27541.939-0.54670.7627-0.0352-0.0205-0.0025-0.01890.08140.0155-0.37770.1563-0.04630.4614-0.10010.03460.1068-0.02460.357727.445397.3559-8.3192
110.01180.06680.01130.593-0.65393.04460.0007-0.0078-0.0167-0.0720.0318-0.108-0.2163-0.0468-0.03250.3814-0.13690.02410.1556-0.02970.302130.362593.537512.4067
120.21220.4213-0.20810.9002-0.59440.7206-0.0740.0219-0.0646-0.03850.0761-0.1048-0.2438-0.1109-0.00210.562-0.12460.05170.11450.07210.386132.928102.8438-5.3654
130.89540.21.01940.20490.09351.36040.0151-0.04520.01790.00350.0077-0.0144-0.18360.0445-0.02280.4593-0.25060.06430.14-0.04580.301436.509498.83789.6961
140.31141.2747-0.11825.3621-0.48410.04930.1295-0.03890.020.5251-0.1234-0.1515-0.0950.024-0.00610.5216-0.1202-0.00610.0435-0.04820.389233.8362106.95943.5106
151.92950.7521-0.50811.3452-0.54511.47550.10360.08910.12940.0950.0983-0.0702-0.4106-0.1516-0.20190.45070.01110.04440.0236-0.01530.360823.310998.282213.8363
161.1750.5913-0.61930.4109-0.20180.45080.07360.1388-0.0281-0.1214-0.0825-0.0212-0.2695-0.20610.00890.52430.17710.01560.215-0.02530.32524.815995.457315.6844
170.32540.1869-0.4220.1561-0.20930.78250.22370.1507-0.03540.19740.0032-0.1039-0.602-0.2391-0.22690.7220.08350.10320.13150.06120.402116.3577101.068818.7396
186.54170.61070.60171.03791.12411.21880.1119-0.18170.1101-0.0701-0.061-0.0463-0.0933-0.068-0.0510.36650.02820.02350.1072-0.03130.304310.619896.798624.387
193.06763.670.07184.52560.53731.52280.5338-0.59030.3190.2617-0.85810.4528-1.1809-0.57580.32421.06610.3343-0.05620.3222-0.19250.47594.736104.938421.0045
200.62351.28190.85352.98521.79321.5139-0.0212-0.10110.2196-0.0431-0.05940.2466-0.3388-0.31620.08060.43770.18550.0520.1872-0.01070.39772.410298.86079.6571
210.99722.770.03818.48761.53272.63450.00910.03740.06790.1359-0.11110.19260.1338-0.33890.1020.2418-0.0446-0.00380.2061-0.01360.24783.927764.121810.4798
220.4970.48750.03320.49290.15851.24870.0812-0.001-0.0340.08840.0031-0.0302-0.0768-0.0338-0.08430.3351-0.0082-0.00270.0943-0.0090.367818.479277.73221.7043
230.6280.021.5780.94310.82784.6140.0184-0.237-0.0240.36180.067-0.03910.3805-0.5456-0.08540.308-0.0920.05640.22230.04460.3364-3.779964.722915.9388
240.76610.33411.04430.22250.17562.73820.1372-0.1945-0.05130.1147-0.1103-0.03640.2562-0.1186-0.02690.391-0.03880.01790.07670.01320.384811.780166.820724.722
251.16541.5171-0.69962.1762-0.56441.1590.0304-0.0636-0.0912-0.0067-0.0311-0.07270.0690.09450.00070.34320.0162-0.020.12150.01250.390320.688270.821415.4018
261.40371.4394-1.45381.6876-1.88633.1324-0.0885-0.0232-0.01370.05180.0002-0.08170.08910.25960.08820.25250.0402-0.00170.1503-0.02940.34134.147674.7206-0.4989
270.32350.6212-0.55451.3028-0.85782.03930.0089-0.0139-0.0563-0.0043-0.0047-0.01720.21060.2727-0.00420.32420.0648-0.02480.10250.01320.396130.422868.092914.0664
280.78961.04560.56721.49131.65398.319-0.00640.01620.07360.02270.05720.06170.11420.4048-0.05080.23680.0475-0.02030.2193-0.01820.285941.228771.6721-2.0391
290.13160.20340.15840.7482-0.78663.2822-0.06760.0701-0.009-0.10080.0543-0.06530.26910.3220.01330.28070.08060.00640.1573-0.04620.304332.563667.50860.5226
302.0348-3.6291.93118.3453-3.81193.5752-0.10820.04520.04110.14970.14510.08180.16330.2396-0.03690.20740.08560.00460.1835-0.08120.216129.474263.3123-0.6691
311.0726-1.74181.29262.8644-1.84783.5273-0.01850.0126-0.02290.0184-0.02070.03480.06120.12950.03920.2738-0.0114-0.02160.1706-0.00710.338822.635168.813-10.1526
322.1453-1.15940.59150.6964-0.54681.23150.0180.0597-0.0796-0.06840.01660.03380.13160.0117-0.03460.3235-0.0023-0.00560.1162-0.04720.369121.209370.214-16.825
334.46291.4919-0.77851.27680.02572.0552-0.08550.2696-0.0691-0.03190.0175-0.03890.0134-0.02010.0680.3092-0.0048-0.00310.09860.02220.278214.85970.8303-24.4597
340.57130.05750.85550.33980.37391.55030.1473-0.0138-0.0486-0.0282-0.0455-0.02720.2754-0.0514-0.10180.42160.02620.0170.0294-0.0060.403420.418461.2146-19.0499
350.8783-1.35770.09973.10650.64460.9967-0.0147-0.0174-0.05770.04260.025-0.01840.1379-0.2389-0.01030.2985-0.04850.0130.169-0.00910.32368.096869.8861-13.2005
361.7694-0.7913-1.40361.09250.73451.3126-0.1284-0.1193-0.0613-0.12060.03170.18320.0919-0.14650.09680.2256-0.0091-0.01790.32520.01360.2958-4.867375.17512.8971
370.955-1.2975-0.71042.212123.06360.02510.0251-0.1458-0.0066-0.08520.17080.1191-0.27750.06010.2676-0.10950.00540.14360.00930.334-1.553467.5343-11.2692
382.0374-0.1994-1.43231.2601-0.25481.145-0.09390.6333-0.0827-0.01230.08840.25210.1261-0.55280.00560.1804-0.24780.00810.58290.00970.2929-9.870766.59532.0387
390.420.07661.7621.51560.62067.56020.1117-0.1405-0.04330.1569-0.00690.13190.3634-0.4833-0.10480.2797-0.11210.0090.2010.00290.2816-2.790459.7698-7.6194
400.34811.19790.50954.5632.32292.3190.04050.00110.00970.0221-0.0096-0.06540.1048-0.3857-0.03090.2397-0.0315-0.01040.20870.03110.28660.369670.71297.8574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 32
2X-RAY DIFFRACTION2A33 - 48
3X-RAY DIFFRACTION3A49 - 72
4X-RAY DIFFRACTION4A73 - 94
5X-RAY DIFFRACTION5A95 - 119
6X-RAY DIFFRACTION6B1 - 27
7X-RAY DIFFRACTION7B28 - 48
8X-RAY DIFFRACTION8B49 - 65
9X-RAY DIFFRACTION9B66 - 93
10X-RAY DIFFRACTION10B94 - 119
11X-RAY DIFFRACTION11C1 - 26
12X-RAY DIFFRACTION12C27 - 50
13X-RAY DIFFRACTION13C51 - 82
14X-RAY DIFFRACTION14C83 - 97
15X-RAY DIFFRACTION15C98 - 120
16X-RAY DIFFRACTION16D1 - 22
17X-RAY DIFFRACTION17D23 - 51
18X-RAY DIFFRACTION18D52 - 66
19X-RAY DIFFRACTION19D67 - 92
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