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- PDB-2rir: Crystal structure of dipicolinate synthase, A chain, from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 2rir
TitleCrystal structure of dipicolinate synthase, A chain, from Bacillus subtilis
ComponentsDipicolinate synthase, A chain
KeywordsOXIDOREDUCTASE / structural genomics / APC1343 / Dipicolinate synthase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / Sporulation
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / sporulation resulting in formation of a cellular spore / oxidoreductase activity
Similarity search - Function
Dipicolinic acid synthetase subunit A / Dipicolinate synthase subunit A, N-terminal / Dipicolinate synthase subunit A N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dipicolinate synthase subunit A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.79 Å
AuthorsOsipiuk, J. / Quartey, P. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis.
Authors: Osipiuk, J. / Quartey, P. / Moy, S. / Joachimiak, A.
History
DepositionOct 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipicolinate synthase, A chain
B: Dipicolinate synthase, A chain
C: Dipicolinate synthase, A chain
D: Dipicolinate synthase, A chain
E: Dipicolinate synthase, A chain
F: Dipicolinate synthase, A chain
G: Dipicolinate synthase, A chain
H: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,36023
Polymers260,1648
Non-polymers6,19515
Water2,180121
1
A: Dipicolinate synthase, A chain
B: Dipicolinate synthase, A chain
C: Dipicolinate synthase, A chain
D: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,16211
Polymers130,0824
Non-polymers3,0807
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
MethodPISA
2
E: Dipicolinate synthase, A chain
F: Dipicolinate synthase, A chain
G: Dipicolinate synthase, A chain
H: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,19812
Polymers130,0824
Non-polymers3,1158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
MethodPISA
3
A: Dipicolinate synthase, A chain
B: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5996
Polymers65,0412
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
MethodPISA
4
C: Dipicolinate synthase, A chain
D: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5635
Polymers65,0412
Non-polymers1,5223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
MethodPISA
5
E: Dipicolinate synthase, A chain
G: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5996
Polymers65,0412
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
MethodPISA
6
F: Dipicolinate synthase, A chain
H: Dipicolinate synthase, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5996
Polymers65,0412
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.578, 75.108, 200.464
Angle α, β, γ (deg.)90.000, 119.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-503-

HOH

DetailsAuthors state that the biological unit of this protein is unknown.

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Components

#1: Protein
Dipicolinate synthase, A chain


Mass: 32520.553 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: spoVFA, dpaA, BSU16730 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04809
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris buffer, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 9, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.79→40 Å / Num. all: 81355 / Num. obs: 81355 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.146 / Χ2: 1.171 / Net I/σ(I): 5.5
Reflection shellResolution: 2.79→2.9 Å / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.37 / Num. unique all: 7396 / Χ2: 0.625 / % possible all: 88.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-2000data reduction
SHELXDphasing
SOLVEphasing
RESOLVEphasing
HKL-2000data scaling
RefinementResolution: 2.79→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 29.656 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.355 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 4079 5 %RANDOM
Rwork0.1986 ---
all0.2011 81346 --
obs0.2011 81346 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-1.27 Å2
2---1.19 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.79→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17942 0 391 121 18454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02218662
X-RAY DIFFRACTIONr_angle_refined_deg1.572.00125397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95452384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81125.22703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.213153264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5571580
X-RAY DIFFRACTIONr_chiral_restr0.110.23104
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213428
X-RAY DIFFRACTIONr_nbd_refined0.2440.28734
X-RAY DIFFRACTIONr_nbtor_refined0.320.212609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2611
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.211
X-RAY DIFFRACTIONr_mcbond_it0.5651.512057
X-RAY DIFFRACTIONr_mcangle_it0.939219096
X-RAY DIFFRACTIONr_scbond_it1.33337186
X-RAY DIFFRACTIONr_scangle_it2.2234.56293
LS refinement shellResolution: 2.79→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 233 -
Rwork0.327 4676 -
all-4909 -
obs-4909 79.65 %
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)
13.1389-0.408-0.71092.5747-2.73715.4030.0515-0.2412-0.1431-0.01410.33550.1065-0.0717-0.5781-0.387-0.0302-0.2652-0.03430.22620.1430.0412153.49912.34660.949
23.59330.48960.79274.044-1.74981.9154-0.13660.1403-0.15760.07450.14680.10890.4579-0.4839-0.0102-0.018-0.29180.00850.33350.1280.0547149.8586.17959.029
31.68920.59371.58271.43460.51943.6958-0.21520.5105-0.0402-0.48410.3606-0.08680.06060.1337-0.14540.0543-0.28590.02730.29640.1194-0.0567160.99211.81750.498
41.43820.1377-0.01642.6017-1.71393.6865-0.2620.0407-0.0669-0.00020.3019-0.1170.1428-0.0214-0.0399-0.033-0.06720.0559-0.00870.00610.0016184.71514.873.673
50.5416-0.8484-0.3394.67940.88223.2204-0.07770.09740.1556-0.22770.1064-0.34160.12080.3547-0.0286-0.0949-0.07360.07140.0756-0.0070.0222193.29719.92965.603
65.0411-0.80560.55560.6146-0.50881.10730.10110.1211-0.0637-0.28020.00110.09250.28970.0012-0.10220.0723-0.14560.0177-0.00440.0219-0.0154174.53312.30761.309
710.1557-0.5696-2.62685.3645-1.82425.953-0.28880.4939-0.41290.07030.32360.02580.09470.3801-0.0348-0.00430.09310.0858-0.1383-0.01220.0134204.132-0.39293.946
85.8210.3399-2.4831.5597-2.61667.2258-0.5754-0.3192-0.39330.01220.3773-0.50710.6260.23040.1981-0.01010.14270.1182-0.154-0.01610.1943207.248-8.14896.572
94.8966-0.36860.94557.74393.75327.7958-0.5819-0.4044-0.88980.24370.33120.48580.7956-0.22740.25070.07250.07110.2424-0.14540.19860.0826196.329-11.108103.831
100.9074-0.5030.47950.8037-0.49510.8366-0.1963-0.1775-0.00430.09180.2130.11650.244-0.1934-0.0167-0.0116-0.01810.07710.01760.06370.0226177.55110.9592.649
113.34741.5405-0.90331.42791.19843.8674-0.0831-0.4117-0.31170.05940.08780.33770.6575-0.6719-0.00460.0272-0.16040.03180.11540.1990.0848165.1522.27592.179
1211.25571.18658.54282.63731.57428.2007-0.2644-0.213-0.1029-0.06010.264-0.3328-0.12960.08110.0004-0.06490.0260.0561-0.09810.00130.0184198.7445.65496.433
1319.07344.360715.257715.687116.300923.3803-0.6779-1.43-1.6527-0.70510.74580.3315-0.4992-1.8198-0.06790.167-0.04860.08320.20160.14840.169152.00429.907112.062
145.1059-0.904-0.65241.4678-1.24953.7423-0.1996-0.26140.24060.0651-0.0444-0.0376-0.3515-0.42510.2440.11110.25390.01080.3566-0.03670.1327157.64441.69113.884
154.5671-5.5007-0.00719.5276-3.081712.2289-1.0798-0.50150.12470.54480.7967-0.387-1.98010.20780.28310.16370.0901-0.02920.2806-0.08280.2633169.10448.223117.808
160.6995-0.1022-0.27350.38680.33211.062-0.2185-0.24760.12870.17260.2122-0.0696-0.0303-0.1710.00630.04020.1311-0.00880.1453-0.01850.089178.62532.295105.945
172.58060.5821.39875.1752-0.6072.3122-0.2302-0.11640.28120.17530.0841-0.4487-0.35580.30660.1461-0.06920.0273-0.060.0181-0.08870.1542197.77536.769100.457
188.38822.8461-3.05031.0733-0.64922.49120.0263-0.3226-0.27880.15-0.1975-0.2174-0.1515-0.09230.17120.08830.16860.0820.16330.00830.1102166.03332.602107.434
193.49392.02911.82586.65530.06916.8131-0.10120.21870.35910.3694-0.1788-0.586-0.140.64220.28-0.1016-0.1342-0.02210.0240.12470.3359202.651.09669.372
203.07910.98482.14353.47311.666310.5997-0.76420.78330.92530.01870.0795-0.2442-0.99371.36990.68470.1415-0.3045-0.16870.08170.32380.4164203.47959.1467.052
216.02561.9366-0.1263.79161.24057.2365-0.78520.54851.2623-0.5830.21680.4865-0.616-0.08890.56840.1856-0.1993-0.2366-0.11240.34820.4377192.10460.72360.701
220.84740.1893-0.42420.2233-0.3422.9239-0.2440.06380.36690.05340.13070.1604-0.4323-0.16010.11330.010.0062-0.0186-0.02990.08090.1974177.8941.64677.583
230.1010.33680.40613.23610.16562.3016-0.18330.02140.1965-0.04750.1720.196-0.0362-0.49660.0114-0.1011-0.023-0.00660.13380.09950.1122166.89634.86175.34
245.5587-0.196-1.37260.7940.26762.4907-0.17160.10.481-0.08340.27030.099-0.4635-0.2289-0.0987-0.00090.0203-0.0098-0.10850.14560.2135175.66147.91774.539
258.063-3.44141.301311.38710.44510.9289-0.10590.7253-0.5147-0.1980.41130.70370.2915-0.321-0.30540.09320.20930.08420.31760.21220.0155172.32622.027151.451
269.7514-6.6873-11.50584.877.187115.3179-1.07830.37680.2016-1.33850.30671.3329-1.2995-0.26240.77160.4376-0.1121-0.06790.44490.14580.4502169.98931.748150.439
272.10111.22692.261811.4638-1.25433.91040.119-0.34940.37541.58980.14020.5822-0.46380.0493-0.25920.61340.35120.24630.15660.01850.1418175.5828.976164.625
281.7959-0.4923-0.18410.3414-0.48931.4303-0.1227-0.2349-0.0030.24630.07050.021-0.4338-0.11270.05230.39460.0795-0.07760.0406-0.05220.054201.8699.531159.477
295.41434.14811.749411.28621.25520.97350.0969-0.6297-0.16170.83140.01620.2587-0.3303-0.1663-0.11310.37810.1456-0.03750.18280.0303-0.0432201.8911.889173.481
305.70060.43271.75120.7259-0.19372.7956-0.1308-0.62160.32110.1680.1089-0.0205-0.6596-0.1020.02190.53960.1866-0.1144-0.0098-0.11930.076199.66117.769165.323
314.5769-0.1154-0.14985.89491.54962.923-0.2284-0.4024-0.0680.15580.3558-0.09660.0876-0.0712-0.12740.37730.2008-0.09260.35530.14440.0172206.593-20.334190.517
322.0721-1.3214-0.61486.9481.21795.4557-0.3607-0.6936-0.16660.70450.73650.6126-0.0383-0.9281-0.37570.43830.27270.06260.67010.3110.0271192.883-19.466196.429
330.7310.15471.32720.8337-0.03972.5382-0.125-0.3339-0.17950.22570.18580.2717-0.0688-0.3475-0.06090.23460.0742-0.01890.27560.15470.1343190.807-12.289165.371
342.6125-0.76810.18454.4456-1.09421.8271-0.009-0.4404-0.0565-0.22190.05380.4902-0.3575-0.7341-0.04490.20770.1563-0.05240.3780.10590.0927179.989-5.551159.715
359.61731.5745-0.75581.76731.45471.710.1513-0.2642-0.4471-0.06110.0380.37410.2102-0.5848-0.18930.1503-0.0099-0.04230.30020.28350.2752176.478-20.26163.421
362.3261-0.01872.13540.68162.10549.6391-0.6438-0.24860.36480.14640.34630.407-0.40930.46260.29760.39150.1524-0.08920.2840.11080.1148201.918-10.703184.366
374.28070.44481.49532.70283.63988.4713-0.0502-0.48840.15410.40060.0618-0.11270.06560.4615-0.01160.2623-0.1112-0.10840.14030.0211-0.0059234.0987.912147.845
383.4494-0.43350.56742.72780.01614.6037-0.0059-0.04910.26820.2249-0.0966-0.0477-0.62920.68960.10250.3516-0.1955-0.13350.13190.03150.075236.46914.449143.912
392.72750.9366-1.54061.5587-0.67282.452-0.03280.0405-0.0233-0.0771-0.0462-0.1299-0.18580.26970.0790.2332-0.0436-0.07770.12640.03750.0316231.7835.451134.227
400.82750.01120.00291.78690.70152.217-0.2172-0.0765-0.0454-0.19730.16410.1878-0.1965-0.0550.05310.24540.0478-0.090.00680.03110.0563199.7280.668140.753
411.7007-0.65790.97092.04110.02654.6409-0.08150.19680.0826-0.36690.09650.0605-0.471-0.2309-0.0150.32430.0541-0.1183-0.07710.0752-0.0311199.5459.488130.461
4213.6859-3.6163-2.61080.9580.61892.5791-0.4935-0.474-0.37540.56110.20.31850.1860.43090.29350.3307-0.0859-0.04620.03240.00740.072228.6372.229146.643
439.59380.2763-0.39892.3529-0.39126.26160.1461-0.02010.02310.4429-0.02130.08470.2138-0.4848-0.12480.1898-0.0539-0.140.01020.06330.0768187.166-31.089131.504
446.59352.8361-2.39342.5431-0.09865.36570.35250.254-0.4098-0.12760.1917-0.20430.6144-0.0667-0.54420.2811-0.0022-0.2758-0.0580.03180.1113187.96-38.516128.403
454.09922.956-1.14334.1593-1.88318.95730.26720.233-1.07390.31410.2091-0.88260.72750.3369-0.47630.27890.1215-0.255-0.1164-0.09920.4497200.578-40.881129.854
460.70660.11921.05190.84811.03334.1469-0.0715-0.1329-0.20660.01730.0608-0.0483-0.1427-0.07950.01070.17620.0161-0.09420.01880.06340.1352204.803-19.904150.614
472.2972-0.615-0.34222.2061-1.22562.44190.0214-0.2467-0.25090.13210.0002-0.21140.180.3531-0.02160.21570.0677-0.14420.06350.03640.0881216.698-22.389156.258
480.8524-0.73712.06251.34040.713313.85630.0418-0.0381-0.20240.0842-0.2784-0.1556-0.82450.02530.23660.222-0.0426-0.10760.02480.05220.0848194.168-23.562132.178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 182 - 21
2X-RAY DIFFRACTION2AA19 - 5622 - 59
3X-RAY DIFFRACTION3AA57 - 13560 - 138
4X-RAY DIFFRACTION4AA136 - 183139 - 186
5X-RAY DIFFRACTION5AA184 - 239187 - 242
6X-RAY DIFFRACTION6AA240 - 295243 - 298
7X-RAY DIFFRACTION7BB0 - 253 - 28
8X-RAY DIFFRACTION8BB26 - 6429 - 67
9X-RAY DIFFRACTION9BB65 - 11368 - 116
10X-RAY DIFFRACTION10BB114 - 202117 - 205
11X-RAY DIFFRACTION11BB203 - 269206 - 272
12X-RAY DIFFRACTION12BB270 - 295273 - 298
13X-RAY DIFFRACTION13CC-1 - 72 - 10
14X-RAY DIFFRACTION14CC8 - 6411 - 67
15X-RAY DIFFRACTION15CC65 - 8168 - 84
16X-RAY DIFFRACTION16CC82 - 19985 - 202
17X-RAY DIFFRACTION17CC200 - 263203 - 266
18X-RAY DIFFRACTION18CC264 - 295267 - 298
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