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- PDB-3gas: Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in C... -

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Basic information

Entry
Database: PDB / ID: 3gas
TitleCrystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme
Componentsheme oxygenase
KeywordsOXIDOREDUCTASE / heme oxygenase / FMN-binding split barrel
Function / homology
Function and homology information


Haem oxygenase, HugZ / PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A ...Haem oxygenase, HugZ / PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / HugZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJiang, F. / Hu, Y.L. / Guo, Y. / Guo, G. / Zou, Q.M. / Wang, D.C.
CitationJournal: To be Published
Title: Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme
Authors: Jiang, F. / Hu, Y.L. / Guo, Y. / Guo, G. / Zou, Q.M. / Wang, D.C.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heme oxygenase
B: heme oxygenase
C: heme oxygenase
D: heme oxygenase
E: heme oxygenase
F: heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,50040
Polymers179,1846
Non-polymers5,31734
Water23,2211289
1
A: heme oxygenase
B: heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,54114
Polymers59,7282
Non-polymers1,81412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-44 kcal/mol
Surface area21810 Å2
MethodPISA
2
C: heme oxygenase
D: heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,41712
Polymers59,7282
Non-polymers1,68910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-51 kcal/mol
Surface area21630 Å2
MethodPISA
3
E: heme oxygenase
F: heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,54114
Polymers59,7282
Non-polymers1,81412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-48 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.330, 139.340, 152.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
heme oxygenase /


Mass: 29863.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: NCTC11639 / Gene: HugZ / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C0LU01, heme oxygenase (biliverdin-producing)
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1289 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, tacsimate, imidazole, methanol, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.00000, 0.97912, 0.97931, 0.96408
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 26, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979121
30.979311
40.964081
ReflectionRedundancy: 9.9 % / Av σ(I) over netI: 7.8 / Number: 810953 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / D res high: 2.321 Å / D res low: 103.142 Å / Num. obs: 82219 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.3457.8399.710.0570.0578.9
5.197.3410010.0520.0529.6
4.245.1910010.0490.0499.8
3.674.2410010.050.059.9
3.283.6710010.0540.05410
33.2810010.0590.05910
2.77310010.0730.07310
2.592.7710010.0880.08810
2.452.5910010.110.119.9
2.322.4510010.1270.1279.7
ReflectionResolution: 1.8→47.87 Å / Num. all: 165619 / Num. obs: 165702 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 20 Å2 / Limit h max: 48 / Limit h min: 0 / Limit k max: 74 / Limit k min: 0 / Limit l max: 76 / Limit l min: 0 / Observed criterion F max: 3093830.4 / Observed criterion F min: 4.1 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 8.621
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.94.50.1724.381539182090.17272.8
1.9-2.015.40.1285.5119174219170.12891.9
2.01-2.157.20.1195.7161041224940.11999.9
2.15-2.327.30.097.4152948210770.09100
2.32-2.557.30.0679.6142096193470.067100
2.55-2.857.40.0512.1130521175990.05100
2.85-3.297.50.04113.4116066155630.041100
3.29-4.027.40.03814.498565132700.038100
4.02-5.697.30.03914.275570103410.039100
5.69-47.896.80.04710.44021358850.04799.5

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.3257.8100753756758
ISO_22.3257.810.5960.421741896719
ISO_32.3257.811.1110.793742636702
ANO_12.3257.811.8480753720
ANO_22.3257.811.3680741630
ANO_32.3257.811.2280742230
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_110.22-57.8100751316
ISO_17.28-10.22001452335
ISO_15.96-7.28001944337
ISO_15.17-5.96002297334
ISO_14.63-5.17002642341
ISO_14.23-4.63002930337
ISO_13.92-4.23003216348
ISO_13.66-3.92003443332
ISO_13.46-3.66003701347
ISO_13.28-3.46003886338
ISO_13.13-3.28004129340
ISO_12.99-3.13004299344
ISO_12.88-2.99004519338
ISO_12.77-2.88004681338
ISO_12.68-2.77004837336
ISO_12.59-2.68005035342
ISO_12.52-2.59005215348
ISO_12.45-2.52005345340
ISO_12.38-2.45005533344
ISO_12.32-2.38005520323
ANO_110.22-57.810.807510
ANO_17.28-10.222.197014520
ANO_15.96-7.283.688019440
ANO_15.17-5.963.133022970
ANO_14.63-5.172.641026420
ANO_14.23-4.632.374029300
ANO_13.92-4.232.291032160
ANO_13.66-3.922.143034430
ANO_13.46-3.662.094037010
ANO_13.28-3.462.105038860
ANO_13.13-3.282.205041290
ANO_12.99-3.132.161042990
ANO_12.88-2.992.114045190
ANO_12.77-2.881.947046810
ANO_12.68-2.771.707048370
ANO_12.59-2.681.654050350
ANO_12.52-2.591.559052150
ANO_12.45-2.521.394053430
ANO_12.38-2.451.219055330
ANO_12.32-2.381.112055190
ISO_210.22-57.810.4730.497749285
ISO_27.28-10.220.6850.6161442332
ISO_25.96-7.281.050.3791925337
ISO_25.17-5.960.8930.6512268334
ISO_24.63-5.170.7770.6352616341
ISO_24.23-4.630.6970.4762894337
ISO_23.92-4.230.6980.4753177348
ISO_23.66-3.920.6640.4743396332
ISO_23.46-3.660.640.4383651347
ISO_23.28-3.460.6530.3863835338
ISO_23.13-3.280.6850.4144068340
ISO_22.99-3.130.6680.4134234344
ISO_22.88-2.990.6270.3824446338
ISO_22.77-2.880.5860.3694610338
ISO_22.68-2.770.5270.3294753336
ISO_22.59-2.680.4970.3044942341
ISO_22.52-2.590.470.3155123348
ISO_22.45-2.520.420.2525244340
ISO_22.38-2.450.3790.265418342
ISO_22.32-2.380.3370.2355398321
ANO_210.22-57.810.95307490
ANO_27.28-10.221.924014390
ANO_25.96-7.282.648019210
ANO_25.17-5.962.19022640
ANO_24.63-5.171.85026140
ANO_24.23-4.631.741028920
ANO_23.92-4.231.673031750
ANO_23.66-3.921.472033960
ANO_23.46-3.661.483036490
ANO_23.28-3.461.479038320
ANO_23.13-3.281.509040680
ANO_22.99-3.131.475042300
ANO_22.88-2.991.413044450
ANO_22.77-2.881.309046070
ANO_22.68-2.771.17047510
ANO_22.59-2.681.101049340
ANO_22.52-2.591.06051130
ANO_22.45-2.520.958052310
ANO_22.38-2.450.86054000
ANO_22.32-2.380.804054530
ISO_310.22-57.810.9820.941747283
ISO_37.28-10.221.6541.0781439331
ISO_35.96-7.281.8460.7661931337
ISO_35.17-5.961.6321.112270334
ISO_34.63-5.171.3951.0562618341
ISO_34.23-4.631.2950.8522898337
ISO_33.92-4.231.2890.9133182348
ISO_33.66-3.921.2280.9133397332
ISO_33.46-3.661.190.7843655347
ISO_33.28-3.461.2280.8383834338
ISO_33.13-3.281.2360.8054074340
ISO_32.99-3.131.1960.7864239344
ISO_32.88-2.991.1230.744454338
ISO_32.77-2.881.050.74611338
ISO_32.68-2.770.9560.6314756335
ISO_32.59-2.680.9050.5674954342
ISO_32.52-2.590.8590.5695128342
ISO_32.45-2.520.770.4455251336
ISO_32.38-2.450.7120.5115429343
ISO_32.32-2.380.6360.4335396316
ANO_310.22-57.810.94307470
ANO_37.28-10.221.952014360
ANO_35.96-7.282.523019270
ANO_35.17-5.962.136022660
ANO_34.63-5.171.773026160
ANO_34.23-4.631.617028960
ANO_33.92-4.231.574031800
ANO_33.66-3.921.411033970
ANO_33.46-3.661.307036530
ANO_33.28-3.461.391038310
ANO_33.13-3.281.385040740
ANO_32.99-3.131.303042350
ANO_32.88-2.991.268044480
ANO_32.77-2.881.146046050
ANO_32.68-2.771.004047470
ANO_32.59-2.680.959049500
ANO_32.52-2.590.909051220
ANO_32.45-2.520.811052390
ANO_32.38-2.450.728054170
ANO_32.32-2.380.676054370
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
164.03935.52513.718SE15.750.77
256.16430.7499.633SE15.110.77
3100.04433.92285.066SE17.650.74
4101.50835.73133.006SE16.190.72
5107.29439.12289.798SE18.310.74
6101.43530.63441.762SE17.340.71
763.36315.09616.029SE19.890.74
866.15254.32817.273SE22.320.77
9103.0415.15332.038SE19.990.72
10104.31554.51330.08SE21.710.73
1152.77511.7638.962SE22.860.78
12101.87311.51244.641SE23.120.74
1397.58254.35886.339SE20.230.7
1496.64114.98785.455SE25.330.77
1554.25351.0612.693SE22.840.73
16106.33518.83493.525SE23.580.72
17108.75658.24992.041SE25.350.74
18106.04750.70142.545SE24.610.72
1933.92355.19515.424SE27.890.7
20113.94314.71112.605SE31.430.71
2129.53259.99815.295SE31.550.68
22116.4369.938116.427SE30.090.65
2333.8985.52515.397SE37.610.68
2477.30160.95595.78SE41.40.73
2564.9228.80737.648SE39.530.66
2677.0219.27890.037SE35.560.61
2732.2819.98120.11SE46.580.73
2872.26665.09395.011SE38.690.65
2968.0674.59641.515SE35.980.61
3074.8914.12393.974SE39.550.61
3169.17949.30118.213SE15.880.26
32103.37649.66626.92SE16.990.24
33101.80916.66447.985SE17.450.22
3449.962177.426SE22.630.26
35111.68353.29493.747SE18.630.21
3694.10319.98283.197SE18.660.24
Phasing dmFOM : 0.85 / FOM acentric: 0.84 / FOM centric: 0.9 / Reflection: 82266 / Reflection acentric: 75488 / Reflection centric: 6778
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-57.8061.310.992.4837692966803
4.1-6.60.950.960.851114198461295
3.3-4.10.940.950.8313810126031207
2.9-3.30.880.890.7113852128321020
2.5-2.90.780.790.5724554229781576
2.3-2.50.670.680.451514014263877

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
SHARPphasing
RESOLVE2.13phasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→47.87 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 3093830 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 8291 5 %RANDOM
Rwork0.192 ---
all-174565 --
obs-165278 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.599 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 74.03 Å2 / Biso mean: 26.662 Å2 / Biso min: 6.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å20 Å20 Å2
2---3.32 Å20 Å2
3----0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11844 0 364 1289 13497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.2527835.20.221143980.009216281518170.2
1.88-1.980.2359685.10.199179660.008216361893487.5
1.98-2.110.243107750.199204390.007217392151699
2.11-2.270.24510504.80.199206240.008217202167499.8
2.27-2.50.23210604.90.19206740.007217702173499.8
2.5-2.860.23611245.20.199206700.007218062179499.9
2.86-3.60.22811155.10.2208380.0072196321953100
3.6-47.870.193111450.178213780.006225322249299.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hem.paramazi.top
X-RAY DIFFRACTION4azi.paramhem.top
X-RAY DIFFRACTION5edo.paramedo.top

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