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- PDB-3bio: Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) ... -

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Basic information

Entry
Database: PDB / ID: 3bio
TitleCrystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83
ComponentsOxidoreductase, Gfo/Idh/MocA family
KeywordsOXIDOREDUCTASE / structural genomics / MCSG / PSI-2 / Gfo/Idh/MocA family / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsNocek, B. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83.
Authors: Nocek, B. / Mulligan, R. / Moy, S. / Joachimiak, A.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2856
Polymers66,6572
Non-polymers6284
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
MethodPISA
2
A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules

A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules

A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,85418
Polymers199,9706
Non-polymers1,88312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.268, 99.268, 356.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-5069-

HOH

21B-1002-

HOH

31B-1167-

HOH

41B-1202-

HOH

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Components

#1: Protein Oxidoreductase, Gfo/Idh/MocA family /


Mass: 33328.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0806 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MW40
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium acetate, 45% MPD, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2007 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 68398 / Num. obs: 68398 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
Cootmodel building
MLPHAREphasing
PHENIXphasing
REFMACphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.667 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3143 5 %RANDOM
Rwork0.156 ---
all0.16 65976 --
obs0.158 62633 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.566 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0.67 Å20 Å2
2---1.34 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 40 433 4860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224534
X-RAY DIFFRACTIONr_bond_other_d0.0020.023088
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9766142
X-RAY DIFFRACTIONr_angle_other_deg0.96837545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28423.548186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07615783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5361539
X-RAY DIFFRACTIONr_chiral_restr0.090.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_nbd_refined0.2130.2805
X-RAY DIFFRACTIONr_nbd_other0.2070.23202
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22152
X-RAY DIFFRACTIONr_nbtor_other0.0850.22519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0580.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.214
X-RAY DIFFRACTIONr_mcbond_it1.0391.53532
X-RAY DIFFRACTIONr_mcbond_other0.2291.51197
X-RAY DIFFRACTIONr_mcangle_it1.21724666
X-RAY DIFFRACTIONr_scbond_it2.43731774
X-RAY DIFFRACTIONr_scangle_it3.4574.51470
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 229 -
Rwork0.181 4329 -
all-4558 -
obs--99.67 %
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)
11.07151.7197-0.94853.3134-0.91663.5183-0.023-0.0284-0.23210.27060.0501-0.36780.07340.041-0.02710.05190.0587-0.02170.01960.03670.11614.797317.1088145.6933
21.53790.5908-2.35443.3805-3.19277.1478-0.0594-0.0682-0.089-0.0771-0.1006-0.31260.13450.15550.15990.03890.02380.0060.03010.00510.14198.901224.3667146.8441
37.052-3.2063-8.79084.58964.599614.07670.0957-0.12330.00730.11830.1188-0.359-0.11270.2208-0.21460.01630.0322-0.01810.01220.02340.08136.657715.7324145.1542
48.56917.182111.949944.77389.484823.3655-1.41531.00770.0276-2.70781.0349-1.2243-1.7591.60.38040.1753-0.0565-0.00510.1610.03180.169515.628214.7912144.4184
52.1186-0.3484-0.44361.75031.18750.9913-0.0224-0.0016-0.14560.0710.0411-0.09010.06140.0195-0.01870.06680.02650.0030.0260.00660.09474.507911.436140.186
65.39232.5847-0.238610.0575-2.22793.33030.01470.3174-0.1113-0.6671-0.1181-0.28850.15930.0660.10350.10410.01920.03030.06140.00340.031-1.049919.3249129.4614
70.4332-0.13640.05682.2575-0.82070.7729-0.01740.0489-0.0679-0.05820.0484-0.0711-0.0256-0.0348-0.0310.08160.00130.01640.038-0.00490.0898-4.296219.8706135.6842
81.05241.0209-0.56774.6771-1.13221.6940.04010.1422-0.1123-0.2594-0.0361-0.01910.0377-0.0893-0.0040.09270.0001-0.00980.0517-0.01080.0535-12.144622.8896131.0065
90.1181-0.07980.01360.39890.10330.03830.00130.0193-0.0271-0.0046-0.01870.02710.0144-0.01120.01750.0878-0.0080.01140.06320.00370.0758-10.124735.2742139.8168
103.9699-0.8938-2.77961.8590.05784.3436-0.08730.1066-0.3042-0.09880.09470.04630.4441-0.1459-0.00740.11810.01280.01620.0425-0.02380.04788.511137.0333126.333
112.0875-0.9045-1.30791.03440.33321.1248-0.04530.05460.0401-0.08860.0330.03220.0050.06370.01230.0821-0.00640.0090.0816-0.00430.03756.836444.827127.7422
123.2828-1.7197-0.26080.9154-0.01031.50950.07160.25780.1485-0.2356-0.0731-0.03150.02190.15320.00150.11750.01480.06020.13030.00780.023216.587943.7118121.2808
1314.16965.3414-3.06956.0068-1.36572.61250.13840.7837-0.0155-0.4327-0.20620.13740.05730.02580.06780.14470.03750.02670.12340.009-0.06868.74144.7919116.7423
144.9064-1.66450.76281.91260.34491.26310.14590.09870.1905-0.313-0.1873-0.12090.07710.00470.04140.07950.00770.03860.08080.01860.00210.245947.2747124.1136
151.78730.90620.16190.5631-0.03970.1579-0.14180.00210.0887-0.01720.1148-0.07740.177-0.01550.0270.08010.0060.01070.07110.00470.056310.307141.6037137.5091
162.5805-0.1464-0.43680.55290.20170.25440.0323-0.00210.0279-0.0333-0.04010.02420.0206-0.04470.00780.07030.00010.00070.06970.00460.0647-17.767350.2605144.029
1715.1483-4.87341.87891.5679-0.60450.233-0.0561-0.13360.59040.0511-0.0012-0.25350.0511-0.06010.05740.09310.01380.0040.0529-0.00720.0777-2.318844.2889146.1302
180.30090.0986-0.33210.089-0.22040.5860.0274-0.0156-0.0281-0.0139-0.0271-0.01950.02340.0345-0.00030.09220.00810.00830.0510.010.07691.671229.1612145.3717
190.8009-0.27590.00060.21960.19141.5042-0.0533-0.0368-0.14850.02830.00960.0554-0.0793-0.06580.04370.0716-0.00690.01670.03960.01080.0969-11.335123.2327147.1517
203.88650.64310.22194.02240.67881.0228-0.0282-0.1418-0.20230.219-0.049-0.07310.07960.10960.07710.1073-0.00610.03140.07240.03650.0187-10.54528.2096161.4369
213.08560.5141-0.83492.5461-0.42370.2588-0.07730.07330.33230.04070.22470.3023-0.114-0.1515-0.14740.00340.03470.02680.10490.03970.0918-34.271643.4084151.9934
222.39241.3458-1.6661.5839-2.49584.09820.09910.17280.07070.01790.21310.1148-0.4093-0.3701-0.312200.05920.02540.11010.06050.0979-36.730641.3176148.2724
2323.963-4.0715-2.01885.83386.45187.42751.573-1.0390.19550.3750.36710.11582.66090.5584-1.94010.2416-0.0128-0.20780.31350.14720.2576-43.940945.8136157.9741
2412.49741.59032.16919.69974.69652.434-0.3533-0.7269-0.54140.410.10.81460.3695-0.4240.2533-0.0580.06320.10820.14490.12660.1199-45.389436.4285158.7509
251.55930.78381.65752.08370.14614.294-0.0752-0.2241-0.03610.25330.09590.2593-0.275-0.3114-0.02070.03680.04920.08480.12490.04070.0461-33.532935.3841161.4415
263.40661.98461.97111.90.53822.2363-0.0084-0.11430.0210.1530.12850.1406-0.0434-0.1806-0.12010.05230.02540.06940.09330.03110.062-31.906131.6301160.4003
270.72840.16930.35892.504-0.3071.84440.0072-0.2222-0.05480.3530.0304-0.0170.0431-0.0065-0.03760.1023-0.01770.02740.10940.0230.0138-19.809231.2008166.3827
280.06990.03770.03740.2478-0.05820.0469-0.0328-0.0929-0.02120.09590.04080.01350.0187-0.0176-0.0080.1015-0.0070.02910.07690.01670.0686-14.034935.7821157.5398
290.5763-1.34570.73745.78381.09443.94660.15860.079-0.19410.2451-0.03670.29840.3167-0.513-0.1220.0584-0.00960.0650.12540.00730.0311-21.450653.317170.177
301.6096-0.6971-0.5281.0710.68240.8451-0.0306-0.1049-0.05910.1368-0.0022-0.0313-0.0814-0.08840.03280.11790.01640.01820.1143-0.0049-0.0014-14.532556.164169.5984
312.9518-1.16020.73940.5187-0.67722.5693-0.2207-0.0886-0.07330.46310.1101-0.0927-0.3426-0.29570.11060.23010.0730.06730.1147-0.0446-0.0209-20.378663.8881175.6998
325.0787-3.5126-1.014710.07252.66822.4605-0.2898-0.4719-0.01560.52910.14170.006-0.0040.03760.14810.1670.03820.01530.1334-0.031-0.0947-15.11458.046180.1377
333.636-2.18560.82413.6551-0.98821.145-0.1138-0.32480.0730.21040.0545-0.0569-0.1495-0.06370.05930.13950.04080.02950.1034-0.0338-0.0554-13.964360.4602172.8777
341.6917-0.7936-0.17621.95360.07340.0184-0.0254-0.0442-0.06930.11970.01940.06060.0648-0.03340.0060.08960.02160.01590.1007-0.00050.005-16.342854.8008158.8087
351.5578-0.5520.00230.1976-0.0460.998-0.04280.0225-0.01440.12440.0462-0.04460.08780.0067-0.00340.10490.00550.01020.05070.01380.06636.36135.2444153.3379
3610.071-0.71320.82534.3915-0.61111.79080.1036-0.0131-0.0133-0.0543-0.0033-0.12260.1261-0.017-0.10020.08240-0.00790.04240.0140.02593.79741.0616150.6537
379.4381-5.7922.22624.0931-0.60161.61050.0177-0.0530.1982-0.0696-0.1266-0.12980.03090.01680.10890.0584-0.00150.01370.0878-0.00530.0471-12.053349.2432151.2209
380.93660.62330.16021.81810.51510.1463-0.0595-0.05670.00080.04860.03090.15750.0115-0.00460.02850.0819-0.00110.02260.0730.00490.0683-25.217241.5608151.3778
390.86630.23980.18830.7403-0.4561.2084-0.05780.0331-0.12270.01790.030.05610.00350.05340.02780.0732-0.00710.02830.04580.00870.0854-21.819828.7406150.2577
402.4719-0.5635-1.56491.4841-0.28861.7729-0.03230.2026-0.1045-0.1227-0.00030.0392-0.0873-0.1820.03260.08280.0057-0.00890.0732-0.00210.0559-19.371333.0309135.8148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 168 - 19
2X-RAY DIFFRACTION2AA17 - 2820 - 31
3X-RAY DIFFRACTION3AA29 - 3932 - 42
4X-RAY DIFFRACTION4AA47 - 5250 - 55
5X-RAY DIFFRACTION5AA53 - 7056 - 73
6X-RAY DIFFRACTION6AA71 - 8174 - 84
7X-RAY DIFFRACTION7AA82 - 9685 - 99
8X-RAY DIFFRACTION8AA97 - 109100 - 112
9X-RAY DIFFRACTION9AA110 - 151113 - 154
10X-RAY DIFFRACTION10AA152 - 162155 - 165
11X-RAY DIFFRACTION11AA163 - 182166 - 185
12X-RAY DIFFRACTION12AA183 - 194186 - 197
13X-RAY DIFFRACTION13AA195 - 207198 - 210
14X-RAY DIFFRACTION14AA208 - 220211 - 223
15X-RAY DIFFRACTION15AA221 - 232224 - 235
16X-RAY DIFFRACTION16AA233 - 247236 - 250
17X-RAY DIFFRACTION17AA248 - 252251 - 255
18X-RAY DIFFRACTION18AA253 - 268256 - 271
19X-RAY DIFFRACTION19AA269 - 291272 - 294
20X-RAY DIFFRACTION20AA292 - 301295 - 304
21X-RAY DIFFRACTION21BB5 - 248 - 27
22X-RAY DIFFRACTION22BB25 - 3828 - 41
23X-RAY DIFFRACTION23BB39 - 5242 - 55
24X-RAY DIFFRACTION24BB53 - 6056 - 63
25X-RAY DIFFRACTION25BB61 - 8064 - 83
26X-RAY DIFFRACTION26BB81 - 9484 - 97
27X-RAY DIFFRACTION27BB95 - 10598 - 108
28X-RAY DIFFRACTION28BB106 - 151109 - 154
29X-RAY DIFFRACTION29BB152 - 161155 - 164
30X-RAY DIFFRACTION30BB162 - 182165 - 185
31X-RAY DIFFRACTION31BB183 - 194186 - 197
32X-RAY DIFFRACTION32BB195 - 207198 - 210
33X-RAY DIFFRACTION33BB208 - 220211 - 223
34X-RAY DIFFRACTION34BB221 - 234224 - 237
35X-RAY DIFFRACTION35BB235 - 243238 - 246
36X-RAY DIFFRACTION36BB244 - 248247 - 251
37X-RAY DIFFRACTION37BB249 - 253252 - 256
38X-RAY DIFFRACTION38BB254 - 270257 - 273
39X-RAY DIFFRACTION39BB271 - 289274 - 292
40X-RAY DIFFRACTION40BB290 - 301293 - 304

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