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- PDB-4n71: X-Ray Crystal Structure of 2-amino-1-hydroxyethylphosphonate-boun... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4n71
TitleX-Ray Crystal Structure of 2-amino-1-hydroxyethylphosphonate-bound PhnZ
ComponentsPredicted HD phosphohydrolase PhnZ
KeywordsOXIDOREDUCTASE / Oxygenase
Function / homology
Function and homology information


2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming) / oxidoreductase activity / hydrolase activity / metal ion binding
Similarity search - Function
HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / [(1R)-2-amino-1-hydroxyethyl]phosphonic acid / 2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming)
Similarity search - Component
Biological speciesuncultured bacterium HF130_AEPn_1 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.984 Å
AuthorsWoersdoerfer, B. / Lingaraju, M. / Yennawar, N. / Boal, A.K. / Krebs, C. / Bollinger Jr, J.M. / Pandelia, M.-E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases.
Authors: Worsdorfer, B. / Lingaraju, M. / Yennawar, N.H. / Boal, A.K. / Krebs, C. / Bollinger, J.M. / Pandelia, M.E.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted HD phosphohydrolase PhnZ
B: Predicted HD phosphohydrolase PhnZ
D: Predicted HD phosphohydrolase PhnZ
E: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,76516
Polymers90,7544
Non-polymers1,01112
Water0
1
A: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9414
Polymers22,6881
Non-polymers2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9414
Polymers22,6881
Non-polymers2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9414
Polymers22,6881
Non-polymers2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9414
Polymers22,6881
Non-polymers2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.761, 65.423, 109.355
Angle α, β, γ (deg.)90.00, 124.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Predicted HD phosphohydrolase PhnZ


Mass: 22688.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium HF130_AEPn_1 (environmental samples)
Gene: ACU83550, ALOHA_HF130_AEPn_1_06c / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0E8I5
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ODV / [(1R)-2-amino-1-hydroxyethyl]phosphonic acid


Mass: 141.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H8NO4P

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 0.2 M ammonium sulphate, 25%(w/v)PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.98→89 Å / Num. obs: 16580 / Biso Wilson estimate: 39 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.984→29.095 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.55 / σ(F): 1.34 / Phase error: 36.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3334 1395 8.42 %
Rwork0.2784 --
obs0.2897 16558 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.0525 Å2
Refinement stepCycle: LAST / Resolution: 2.984→29.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 40 0 5764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085897
X-RAY DIFFRACTIONf_angle_d0.4527937
X-RAY DIFFRACTIONf_dihedral_angle_d10.8292208
X-RAY DIFFRACTIONf_chiral_restr0.033812
X-RAY DIFFRACTIONf_plane_restr0.0021023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.984-3.09060.39231400.34951509X-RAY DIFFRACTION94
3.0906-3.21420.46161420.33781548X-RAY DIFFRACTION96
3.2142-3.36030.37741430.33131531X-RAY DIFFRACTION96
3.3603-3.53710.39761420.30431544X-RAY DIFFRACTION94
3.5371-3.75830.41481360.29181508X-RAY DIFFRACTION94
3.7583-4.04780.36511390.27691516X-RAY DIFFRACTION93
4.0478-4.45380.29231370.2541482X-RAY DIFFRACTION91
4.4538-5.09530.30921360.26131470X-RAY DIFFRACTION90
5.0953-6.40830.3271340.28041472X-RAY DIFFRACTION89
6.4083-29.0960.24741460.251583X-RAY DIFFRACTION94
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)
15.33943.2316-3.2786.4913-4.54333.2837-0.48380.79880.6668-1.21930.88561.61561.1895-0.2618-0.37670.3129-0.1447-0.00540.54820.04710.522148.775537.94976.0138
21.98825.8711-1.53646.7971-0.80450.2557-0.29290.65780.94430.6839-0.43590.89330.99790.4901-0.6980.5973-0.1285-0.00330.5549-0.03680.234461.007248.3561.2159
32.0287-1.233.36439.5769-7.99877.3032-1.12021.09780.2482-0.7048-1.0173-1.85330.72351.67730.86350.61640.1988-0.02830.7521-0.04520.487165.538335.01454.4843
45.8010.6388-1.33195.557-2.22411.50270.3472-0.74960.3664-0.2869-0.51070.65890.30130.72670.08710.3652-0.0394-0.03240.55770.01420.345258.123343.345614.2867
52.7534-0.3853-1.5740.9798-0.33322.275-1.0792-1.0266-0.76551.82620.53260.19060.34780.301-0.03160.72650.0599-0.26410.697-0.01450.172959.176537.189220.9135
67.7184-3.23615.1215.8038-2.96396.26260.20441.36910.3046-0.5898-0.339-0.23150.22671.52560.36050.26650.0651-0.06840.7855-0.01850.505773.144650.541814.0326
75.6482-3.8988-0.98775.2296-4.11818.93250.3827-1.47020.29111.6133-0.1474-0.1585-0.04341.7907-0.050.4632-0.0887-0.22110.8187-0.10980.755672.910345.909727.3996
81.7969-0.8967-0.9352.3082-0.20374.47050.2259-0.0545-0.4643-0.5726-0.1238-0.13791.20531.2741-0.06580.57730.1011-0.07650.11640.04580.795462.583834.03249.366
95.5261-4.42543.79768.572-3.33444.3515-0.1097-0.6745-0.1945-0.45450.51120.0339-0.0868-0.6352-0.35230.4677-0.1481-0.02580.6002-0.02720.292257.95768.806435.6252
105.93740.3279-3.06367.02342.64982.83690.25940.5776-0.582-0.6271-0.3129-0.2147-0.7257-0.49690.17770.5844-0.1139-0.08180.4780.04080.351258.11985.749926.9103
112.18182.097-0.61819.1251-1.56545.1313-0.26531.12160.5727-0.519-0.18740.798-0.5031-0.35880.3920.50150.0045-0.12660.58450.08560.497152.30058.463521.2215
124.7175-5.15641.56156.344-4.07798.7203-0.21360.11781.78260.97-0.2218-1.4506-0.54750.72020.40670.577-0.11370.00440.481-0.16350.686172.96746.406719.4039
132.2459-1.4221.72943.9197-4.03674.2066-0.14240.8377-0.0129-0.80290.9379-0.1435-0.50321.2662-0.26030.6628-0.0783-0.0550.65220.09590.596870.1614-1.901320.029
148.4882-2.08910.07112.49852.44327.8377-0.2667-0.35240.5582-0.15310.0982-0.0647-1.58450.4861-0.09380.6424-0.18750.0770.4697-0.03930.611166.723812.275621.0698
158.9615.1942.29982.07277.05084.7117-0.7252-0.20911.7754-0.2495-0.22680.4333-0.858-0.42650.89290.58090.15950.0990.73820.04230.749448.777618.956632.0621
163.60680.566-2.92624.8714-1.00262.979-0.23920.165-0.0678-0.0721-0.2095-0.53330.2923-0.72620.46530.26530.04730.01870.73220.00020.676937.30336.81783.2204
171.96860.95170.63313.14361.85256.252-0.0440.18540.1427-1.65090.31760.732-0.2722-0.552-0.29420.5576-0.0254-0.03690.31920.12620.695122.31933.42671.0588
180.0769-0.1502-0.06750.82751.78985.03010.4215-0.03112.7438-0.14790.65420.40230.9236-0.7891-0.43040.3767-0.27070.10940.6404-0.06841.234923.057744.95889.6839
190.22410.58410.5433.79120.05832.29120.5402-0.850.1646-1.3884-2.7022-0.3496-0.02770.87580.26650.4838-0.30920.83730.5820.9277-0.681427.864825.49711.3054
202.0088-2.309-0.42876.48320.28441.0064-0.32690.12980.86140.1072-0.2210.76010.27780.07820.37420.30920.0713-0.12280.63310.05060.662832.268935.035416.462
213.2281-0.3676-0.46653.5393-0.24051.5201-0.54740.8767-0.16160.19940.38460.2523-0.05340.71220.11240.42460.09780.02120.6393-0.11160.343219.512934.339517.9812
226.0429-3.2373-0.35788.52051.79764.8709-0.49820.0447-0.72060.74670.2821.86361.5961-0.88150.03710.6660.50580.19231.06580.27290.79257.125527.348811.2592
233.77161.4036-3.18665.903-5.21225.82430.0735-1.7229-0.4374-0.8540.98110.95890.90031.1441-0.49750.3540.1495-0.05220.73390.07580.690315.521421.642414.9494
244.72274.4692-3.6526.1715-3.26978.7684-0.8434-0.3350.9962-1.16952.17981.65320.23310.1727-0.42060.78370.19020.11240.7987-0.12320.61613.602134.789926.9102
258.4232-5.6027-4.94247.52023.98073.0373-0.4105-0.86790.3910.1721.53890.2356-0.48541.7295-0.68280.3843-0.0665-0.01430.4745-0.03560.689215.111537.944512.2538
266.45614.3339-4.67555.7223-5.92736.1362-1.07091.18142.04470.4897-0.401-0.7235-0.19970.0470.61760.717-0.3079-0.12730.03510.14480.753118.80436.4179-4.7994
270.84931.10851.67973.83534.81327.70650.32470.33370.0446-0.88540.8925-0.566-0.70360.9319-0.91540.4146-0.17990.07910.45170.06030.659533.407646.99526.6935
284.3047-3.8838-5.03856.36512.40516.69920.824-1.8882-1.2483-1.1202-0.05-0.1803-0.25690.712-0.46270.5517-0.0018-0.11350.47110.10950.600936.88315.366239.3478
294.8195-2.8034-2.36128.648-3.78744.9739-0.2965-0.5684-0.89681.72450.80931.4382-0.4395-0.0487-0.49520.4713-0.063900.66520.15290.615221.2724.856937.5594
304.2841-1.08530.10428.0807-2.21934.862-0.0850.0280.04750.1361-0.3001-1.0042-0.29351.77960.14020.6823-0.0803-0.07260.7881-0.08330.285226.80686.03829.1868
317.2851.51514.28014.4791.06857.0782-0.28191.29751.44660.29850.01840.60481.27710.61360.21690.4519-0.04250.02710.26740.04410.630833.19753.557823.9994
322.29393.2793-2.56696.3648-3.2726.3927-0.25070.86850.39150.58470.43750.2859-0.4939-0.25830.00330.3476-0.03520.00920.4835-0.0120.439413.86779.051822.4375
332.96650.41890.26053.65761.850.8162-0.1442-0.16130.01670.1019-0.1695-0.3898-0.38920.46950.17220.43430.06-0.09880.370.02840.480218.47470.938322.9363
340.24610.1931.240.90421.82977.061-0.8005-0.6273-0.88180.11531.08190.4872-0.08221.9093-0.15440.54920.3413-0.18670.8676-0.04260.737736.3962-5.736135.9682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 103 )
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 133 )
7X-RAY DIFFRACTION7chain 'A' and (resid 134 through 150 )
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 188 )
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 103 )
12X-RAY DIFFRACTION12chain 'B' and (resid 104 through 123 )
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 138 )
14X-RAY DIFFRACTION14chain 'B' and (resid 139 through 173 )
15X-RAY DIFFRACTION15chain 'B' and (resid 174 through 188 )
16X-RAY DIFFRACTION16chain 'D' and (resid 4 through 21 )
17X-RAY DIFFRACTION17chain 'D' and (resid 22 through 44 )
18X-RAY DIFFRACTION18chain 'D' and (resid 45 through 56 )
19X-RAY DIFFRACTION19chain 'D' and (resid 57 through 79 )
20X-RAY DIFFRACTION20chain 'D' and (resid 80 through 94 )
21X-RAY DIFFRACTION21chain 'D' and (resid 95 through 112 )
22X-RAY DIFFRACTION22chain 'D' and (resid 113 through 123 )
23X-RAY DIFFRACTION23chain 'D' and (resid 124 through 138 )
24X-RAY DIFFRACTION24chain 'D' and (resid 139 through 150 )
25X-RAY DIFFRACTION25chain 'D' and (resid 151 through 163 )
26X-RAY DIFFRACTION26chain 'D' and (resid 164 through 173 )
27X-RAY DIFFRACTION27chain 'D' and (resid 174 through 188 )
28X-RAY DIFFRACTION28chain 'E' and (resid 4 through 21 )
29X-RAY DIFFRACTION29chain 'E' and (resid 22 through 44 )
30X-RAY DIFFRACTION30chain 'E' and (resid 45 through 79 )
31X-RAY DIFFRACTION31chain 'E' and (resid 80 through 103 )
32X-RAY DIFFRACTION32chain 'E' and (resid 104 through 133 )
33X-RAY DIFFRACTION33chain 'E' and (resid 134 through 173 )
34X-RAY DIFFRACTION34chain 'E' and (resid 174 through 188 )

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