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- PDB-6mg6: Crystal structure of carbon-nitrogen hydrolase from Helicobacter ... -

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Basic information

Entry
Database: PDB / ID: 6mg6
TitleCrystal structure of carbon-nitrogen hydrolase from Helicobacter pylori G27
ComponentsCarbon-nitrogen hydrolase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Helicobacter pylori / CN-hydrolase / Carbon-Nitrogen hydrolase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


: / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbon-nitrogen hydrolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of carbon-nitrogen hydrolase from Helicobacter pylori G27
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 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: Carbon-nitrogen hydrolase
B: Carbon-nitrogen hydrolase
C: Carbon-nitrogen hydrolase
D: Carbon-nitrogen hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,5575
Polymers137,4614
Non-polymers961
Water7,080393
1
A: Carbon-nitrogen hydrolase
B: Carbon-nitrogen hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8273
Polymers68,7312
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-37 kcal/mol
Surface area20710 Å2
MethodPISA
2
C: Carbon-nitrogen hydrolase
D: Carbon-nitrogen hydrolase


Theoretical massNumber of molelcules
Total (without water)68,7312
Polymers68,7312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-28 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.580, 91.380, 95.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 0 and (name N or name...
21(chain B and (resid 0 through 16 or (resid 17...
31(chain C and (resid 0 through 16 or (resid 17...
41(chain D and (resid 0 through 31 or (resid 32...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and ((resid 0 and (name N or name...AA08
12HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
13HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
14HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
15HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
21HISHISLYSLYS(chain B and (resid 0 through 16 or (resid 17...BB0 - 168 - 24
22LYSLYSLYSLYS(chain B and (resid 0 through 16 or (resid 17...BB1725
23HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
24HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
25HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
26HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
31HISHISLYSLYS(chain C and (resid 0 through 16 or (resid 17...CC0 - 168 - 24
32LYSLYSLYSLYS(chain C and (resid 0 through 16 or (resid 17...CC1725
33HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
34HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
35HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
36HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
41HISHISLYSLYS(chain D and (resid 0 through 31 or (resid 32...DD0 - 318 - 39
42LYSLYSLYSLYS(chain D and (resid 0 through 31 or (resid 32...DD3240
43HISHISARGARG(chain D and (resid 0 through 31 or (resid 32...DD-3 - 2905 - 298
44HISHISARGARG(chain D and (resid 0 through 31 or (resid 32...DD-3 - 2905 - 298
45HISHISARGARG(chain D and (resid 0 through 31 or (resid 32...DD-3 - 2905 - 298

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Components

#1: Protein
Carbon-nitrogen hydrolase / HepyC.18002.a.B1


Mass: 34365.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_713
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B5Z7B9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, G8: 25% PEG 3350, 200mM Ammonium sulfate, 100mM Tris Base/HCl pH 8.5: HepyC.18002.a.B1.PS38436 at 19.87mg/ml: cryo: 15% EG: tray 3301220G8: puck eko9-11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.1→47.576 Å / Num. obs: 70182 / % possible obs: 99.4 % / Redundancy: 6.543 % / Biso Wilson estimate: 50.265 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.974 / Net I/σ(I): 25.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.670.5433.3651700.8930.589100
2.15-2.216.4190.444.0450260.9180.479100
2.21-2.286.5270.3515.6945670.9590.38193.8
2.28-2.356.7170.2846.4247730.9660.30899.9
2.35-2.426.4370.2227.9746040.9760.24299.9
2.42-2.516.9050.17610.2744660.9880.191100
2.51-2.66.8540.1511.9643090.9910.16299.8
2.6-2.716.7050.11515.3441500.9940.12599.9
2.71-2.836.3390.09218.2239780.9960.10199.9
2.83-2.976.6630.06824.4138320.9980.07499.8
2.97-3.136.4540.05529.5436330.9980.05999.7
3.13-3.326.5530.0438.8734350.9990.04399.9
3.32-3.556.7220.03147.1932520.9990.03499.7
3.55-3.836.4150.02854.3830300.9990.03199.4
3.83-4.26.1390.02459.5327900.9990.02699.6
4.2-4.76.3890.02165.1255010.02399.6
4.7-5.426.4830.02267.1522550.9990.02499.6
5.42-6.646.4390.02365.5819370.9990.02599.8
6.64-9.395.9950.0268.66153510.02299.7
9.39-47.5765.6790.01770.388900.9990.01998.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
PARROTphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5h8iA as per Morda

Resolution: 2.1→47.576 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 2044 2.91 %0
Rwork0.1679 ---
obs0.169 70175 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.64 Å2 / Biso mean: 55.9961 Å2 / Biso min: 19.53 Å2
Refinement stepCycle: final / Resolution: 2.1→47.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9123 0 5 393 9521
Biso mean--83.13 50.18 -
Num. residues----1172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079379
X-RAY DIFFRACTIONf_angle_d0.84512732
X-RAY DIFFRACTIONf_dihedral_angle_d12.2735483
X-RAY DIFFRACTIONf_chiral_restr0.0581367
X-RAY DIFFRACTIONf_plane_restr0.0061660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5057X-RAY DIFFRACTION5.504TORSIONAL
12B5057X-RAY DIFFRACTION5.504TORSIONAL
13C5057X-RAY DIFFRACTION5.504TORSIONAL
14D5057X-RAY DIFFRACTION5.504TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.25131610.218944964657100
2.1489-2.20260.2531380.221144964634100
2.2026-2.26220.42371400.33724225436594
2.2622-2.32870.27031340.206244994633100
2.3287-2.40390.23591310.193645094640100
2.4039-2.48980.20641400.176645204660100
2.4898-2.58950.22551350.18345214656100
2.5895-2.70730.26461300.184645564686100
2.7073-2.850.24141350.183845364671100
2.85-3.02860.2191370.185245424679100
3.0286-3.26240.19621420.183845654707100
3.2624-3.59060.2071450.169645554700100
3.5906-4.10990.17881300.1454594472499
4.1099-5.1770.15950.12846804775100
5.177-47.58860.19651510.160648374988100
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)
12.34250.11040.5945.08361.09173.0001-0.1254-0.4818-0.52510.47920.0913-0.10870.21010.07160.03720.36010.06030.04870.41690.19280.43056.610119.49326.3782
22.7975-0.66210.49393.05670.59641.9461-0.1576-0.2856-0.37550.28490.0852-0.4290.1220.25510.08170.25860.02890.0120.36470.12640.376813.720427.759720.0717
32.37350.12260.93553.1679-0.08740.9617-0.1454-0.4702-0.21640.34560.1686-0.02310.0338-0.08410.0240.21680.01230.0310.30720.05850.2489-1.639631.524117.6945
43.58720.0432-2.49572.8933-0.54128.70260.1162-0.9073-0.57780.42930.08020.3005-0.2184-0.2524-0.10380.2856-0.00950.07310.49180.18540.4276-13.927825.977223.0078
52.20990.30260.91231.48990.08853.91850.0022-0.7457-0.44610.53120.05890.08880.1711-0.4392-0.01960.40990.08380.08720.51330.19340.413-4.857423.234327.8687
62.189-0.80940.83370.7398-0.07211.88420.10590.0315-0.4832-0.1856-0.11420.13830.3108-0.0876-0.01750.2411-0.09350.03730.240.02990.3384-11.730425.16675.7614
72.4223-0.20550.71732.31410.24581.95730.1234-0.4825-0.25760.4752-0.06330.74680.5262-0.53150.05030.3394-0.0490.0950.60270.16690.6464-40.140929.719113.7792
82.878-0.04932.0132.54981.36322.67390.2888-0.7054-0.41210.2797-0.04010.98020.5841-1.6341-0.09670.315-0.09080.05160.72380.08870.8735-48.858929.249311.5445
91.91550.37631.31953.05421.7593.6438-0.1981-0.4353-0.5144-0.17380.15530.3934-0.02350.13190.11710.3029-0.0437-0.03030.47630.14620.5989-38.215328.05845.8145
105.8032-2.7634-3.67053.8483.10915.7582-0.1897-0.0594-0.3193-0.2432-0.11030.9041-0.1639-0.55070.39040.3245-0.0295-0.10350.54620.09970.6496-44.633134.3078-1.0317
113.49510.34870.46231.94420.71433.589-0.21530.0266-0.2877-0.19040.14780.39580.0718-0.2230.07470.2681-0.0326-0.04420.26140.07490.3944-32.335934.4959-0.9786
122.25380.58910.65740.49770.24041.8305-0.0997-0.2482-0.46110.13510.14580.31540.2147-0.1607-0.02850.2157-0.02810.0030.22090.05650.3319-25.591232.41598.8966
133.38861.88930.58572.04650.07752.51210.0554-0.3537-0.7335-0.05210.06050.20410.4228-0.2881-0.12150.3118-0.05520.00590.36440.13290.4478-22.07121.536614.439
142.72061.55251.23762.92142.15623.09720.1228-0.2956-0.61320.25990.02130.3350.5486-0.3378-0.15470.3737-0.04710.0160.42570.19590.5897-32.431621.829511.952
153.64344.03560.5234.44870.66021.00260.2348-1.08120.00110.3777-0.320.47820.1362-0.39690.04610.38480.00790.07060.61410.04170.406-26.739237.793624.3881
163.4850.95441.03393.84992.7512.5554-0.1463-0.1645-0.0642-0.01620.2097-0.12220.23360.1603-0.00630.2273-0.0018-0.01190.22150.06150.2525-6.699437.58548.8508
172.09660.4598-0.18792.8081-1.70473.8027-0.02610.617-0.6336-0.6448-0.0731-0.18440.5240.59250.08090.6172-0.01670.03920.6835-0.29530.5602-7.905514.1799-29.0251
182.7973-1.306-1.17243.91830.38545.58550.04190.4995-0.7441-0.25250.1304-0.64080.43590.8823-0.04020.4050.04070.01180.5452-0.21830.615-3.006313.0696-18.0374
191.0425-0.71450.61223.1314-0.8261.948-0.02660.4511-0.2667-0.41210.0609-0.0352-0.02280.1995-0.02370.4057-0.1260.00840.497-0.11580.3472-11.396726.0866-20.9301
206.59171.82872.0285.51532.48624.6980.26850.5512-0.8006-0.4814-0.0519-0.142-0.12240.364-0.25750.7188-0.1089-0.16490.6876-0.0440.4413-24.177428.0538-33.1536
211.708-0.22480.13422.3470.65411.2114-0.09570.5878-0.5122-0.83940.14850.00850.32670.2506-0.11330.6359-0.1395-0.07360.6476-0.17690.4297-18.729319.0537-31.591
223.1717-0.3449-0.41946.6273-0.44262.1772-0.11021.10190.1303-1.446-0.2216-0.5513-0.55250.67740.25971.1289-0.21260.12620.9846-0.04980.4339-7.260432.0227-40.5875
233.9539-0.1902-0.47393.5751-0.33841.85750.20880.58610.4213-0.43760.007-0.4532-0.76690.1769-0.17670.7805-0.1945-0.02320.5310.0260.4716-19.87748.1707-23.5251
241.9905-0.87530.30194.6002-0.38443.54070.44240.87850.2366-0.2513-0.00220.2937-0.5464-0.5457-0.33560.927-0.0866-0.19551.0410.29170.5596-41.867152.0317-41.2926
252.0707-1.38011.22893.3975-1.22783.60.00650.66450.6078-0.55290.0694-0.1005-0.78530.1333-0.08110.9857-0.0472-0.02240.70910.20980.6316-34.744659.857-33.516
262.0631-0.2135-0.47182.0924-1.00413.08730.10510.93330.3366-0.94930.0434-0.08490.1383-0.0142-0.18980.8924-0.1037-0.07790.71480.11160.3808-28.133245.1506-38.2308
272.5628-1.45751.92641.0014-1.19573.8311-0.10710.466-0.1792-0.69560.30530.35150.1284-0.2643-0.2750.6886-0.2066-0.15760.52010.02750.3572-31.396636.1537-26.6673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 55 )A-1 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 114 )A56 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 185 )A115 - 185
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 207 )A186 - 207
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 254 )A208 - 254
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 292 )A255 - 292
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 14 )B0 - 14
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 32 )B15 - 32
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 55 )B33 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 79 )B56 - 79
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 139 )B80 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 185 )B140 - 185
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 207 )B186 - 207
14X-RAY DIFFRACTION14chain 'B' and (resid 208 through 254 )B208 - 254
15X-RAY DIFFRACTION15chain 'B' and (resid 255 through 272 )B255 - 272
16X-RAY DIFFRACTION16chain 'B' and (resid 273 through 292 )B273 - 292
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 55 )C0 - 55
18X-RAY DIFFRACTION18chain 'C' and (resid 56 through 79 )C56 - 79
19X-RAY DIFFRACTION19chain 'C' and (resid 80 through 185 )C80 - 185
20X-RAY DIFFRACTION20chain 'C' and (resid 186 through 207 )C186 - 207
21X-RAY DIFFRACTION21chain 'C' and (resid 208 through 254 )C208 - 254
22X-RAY DIFFRACTION22chain 'C' and (resid 255 through 272 )C255 - 272
23X-RAY DIFFRACTION23chain 'C' and (resid 273 through 292 )C273 - 292
24X-RAY DIFFRACTION24chain 'D' and (resid -3 through 55 )D-3 - 55
25X-RAY DIFFRACTION25chain 'D' and (resid 56 through 144 )D56 - 144
26X-RAY DIFFRACTION26chain 'D' and (resid 145 through 240 )D145 - 240
27X-RAY DIFFRACTION27chain 'D' and (resid 241 through 290 )D241 - 290

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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