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- PDB-9ebk: Piperazate synthase (PipS) in complex with haem -

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Basic information

Entry
Database: PDB / ID: 9ebk
TitlePiperazate synthase (PipS) in complex with haem
ComponentsPiperazate synthase
KeywordsBIOSYNTHETIC PROTEIN / N-N bond / natural product biosynthesis / heme / piperazate / piperazic acid
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces griseus subsp. griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08006722536 Å
AuthorsHiggins, M.A. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RPGIN-2021-02626 Canada
CitationJournal: Nat Catal / Year: 2025
Title: Structure and mechanism of haem-dependent nitrogen-nitrogen bond formation in piperazate synthase
Authors: Higgins, M.A. / Shi, X. / Soler, J. / Harland, J.B. / Parkkila, T. / Lehnert, N. / Garcia-Borras, M. / Du, Y.L. / Ryan, K.S.
History
DepositionNov 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Piperazate synthase
A: Piperazate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6295
Polymers50,3042
Non-polymers1,3253
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-86 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.510, 66.510, 478.694
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-640-

HOH

21B-658-

HOH

31B-677-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11METMETILEILE(chain 'A' and (resid 1 through 19 or resid 21...AB1 - 191 - 19
12GLYGLYPROPRO(chain 'A' and (resid 1 through 19 or resid 21...AB21 - 21421 - 214
13HISHISHISHIS(chain 'A' and (resid 1 through 19 or resid 21...AB221 - 223221 - 223
24METMETILEILE(chain 'B' and (resid 1 through 19 or resid 21...BA1 - 191 - 19
25GLYGLYPROPRO(chain 'B' and (resid 1 through 19 or resid 21...BA21 - 21421 - 214
26HISHISHISHIS(chain 'B' and (resid 1 through 19 or resid 21...BA222 - 224222 - 224

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Components

#1: Protein Piperazate synthase


Mass: 25152.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus subsp. griseus (bacteria)
Strain: NRRL F-5144 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.76 M sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.08→79.78 Å / Num. obs: 39715 / % possible obs: 100 % / Redundancy: 33.7 % / Biso Wilson estimate: 34.570676426 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.044 / Net I/σ(I): 15.3
Reflection shellResolution: 2.08→2.14 Å / Num. unique obs: 2987 / CC1/2: 0.882 / Rpim(I) all: 0.476

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08006722536→79.78 Å / SU ML: 0.231386837288 / Cross valid method: FREE R-VALUE / σ(F): 1.33571543112 / Phase error: 22.7598007899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227741031055 1982 5.01594371615 %
Rwork0.188418974756 37532 -
obs0.190428077865 39514 99.9645820684 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.39028751 Å2
Refinement stepCycle: LAST / Resolution: 2.08006722536→79.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 92 167 3627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008569452277693584
X-RAY DIFFRACTIONf_angle_d1.1719104814914
X-RAY DIFFRACTIONf_chiral_restr0.0595601690564511
X-RAY DIFFRACTIONf_plane_restr0.00665384220437637
X-RAY DIFFRACTIONf_dihedral_angle_d13.28272678962434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0801-2.13210.351895581471380.2830410980142586X-RAY DIFFRACTION99.9633027523
2.1321-2.18970.3149171058811340.2523925140122568X-RAY DIFFRACTION99.9630040696
2.1897-2.25420.2991504742421360.255969608542623X-RAY DIFFRACTION99.8552298227
2.2542-2.32690.310794161461440.2457215979892606X-RAY DIFFRACTION99.963649582
2.3269-2.41010.2980900643251400.2390338241362634X-RAY DIFFRACTION99.9279538905
2.4101-2.50660.2564066035051390.2258530388432608X-RAY DIFFRACTION99.9636098981
2.5066-2.62070.3022932679471210.213388066992660X-RAY DIFFRACTION100
2.6207-2.75890.2439199245951350.2144918522672676X-RAY DIFFRACTION99.9644381223
2.7589-2.93170.232467470391380.2084872213072642X-RAY DIFFRACTION100
2.9317-3.15810.2503865212921340.2091131363732694X-RAY DIFFRACTION100
3.1581-3.47590.2299922913381400.1810491900982706X-RAY DIFFRACTION99.9648753073
3.4759-3.97890.1951868174571490.154169253892715X-RAY DIFFRACTION100
3.9789-5.01290.1755926702591640.1333581686792781X-RAY DIFFRACTION100
5.0129-79.780.2006781641691700.1796899860473033X-RAY DIFFRACTION99.9375975039
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)
12.13855627133-1.437299488621.361689090872.41190068756-1.544190341886.214032494160.1419596747770.101413618836-0.0141265156707-0.0293690587576-0.0644191200819-0.03298239317030.04143567681160.240438675059-0.0726929749430.118917772171-0.03009277510940.04755596764890.288657051668-0.06263310100340.248626193528-15.271803502615.6653469883-9.9612133995
27.20595371471-0.4025911910244.034079376525.3996538812-0.899772937963.0394713414-0.100064829580.614035325606-1.29132609371-0.131725586674-1.246312832260.6777849945721.021522721330.005636798700791.1514673880.4676862117110.1582823885590.01707464658971.09981348158-0.2950085082140.91103356189-8.579270191964.42900133762-17.0439068357
32.933432831190.05597700109750.1692262217931.948730278570.2790631653734.993644918870.1443338451110.453306232837-0.307115156693-0.28902611668-0.0266525068947-0.01927469030470.1096500614210.29050129093-0.0734164732710.2059637167430.06848218727320.004955952199630.307606725428-0.100698733720.294930008951-19.327759630913.148118538-17.6906755464
45.647421707221.83639582394-1.328250006514.84705448609-1.02251646359.52585870215-0.121323035558-1.33431591048-0.8483148199390.9134926700930.05900991961560.2866510953970.355170115569-0.439087435114-0.06237390297390.4885420929720.002745742076120.09381249127290.5765576294150.09929240249240.433814199809-23.13868510328.259161730811.7849443055
58.50425737541-3.320908554041.403709608167.687063198042.480164472546.662289553550.0291473148368-1.01486507166-0.2825726286890.659813287470.3422160685290.2123814517750.190874786239-0.380561001334-0.4571841868260.493541353582-0.09363327682580.1101107226070.4411441377820.09114461332410.378254612843-22.32920015719.257108473475.3155896649
65.22069570526-3.45905506198-4.202374724985.095513414161.808422818137.563377056340.3510904826560.256822857110.134485115197-0.658771792675-0.6062828313060.77172087111-0.689385236387-0.5842379900350.2969931829920.3467752378270.039368971643-0.07258938104480.422536352854-0.07037811943520.320587380324-34.555974507824.9747671471-20.8053148784
70.553353869378-0.6175043547481.168825490212.940597506250.1633219634033.121495242270.0275596124175-0.1402688432870.018137696726-0.029223985332-0.0608921173374-0.150781046278-0.08322786127040.09222976256640.04203995188710.180875015096-0.06390553013020.04439410201250.30449743192-0.07050600796010.246742906208-22.970657768426.20881135-6.8952438327
87.55666347631-2.924842137651.777254593716.17841456951-0.9260297746127.13938450246-0.452287289701-1.233071411110.717036191525-0.239207646281-0.2305002261730.07402392007-0.671971252825-1.171971138090.6414652002370.2893928573220.0595260551857-0.01707697857070.557825946708-0.1109311146770.392444144773-34.880038889937.9808063652-3.72249190797
92.08844580760.008773599221141.246988355371.326910430780.8801974800593.675383803340.002022793931390.2376895645540.166860903121-0.1208677018510.10994540808-0.00937097062797-0.09995379634170.147355987403-0.1221548699240.157186071669-0.01478654698380.05576604384730.302360795885-0.05113877007960.27561192467-23.765581716823.9692686657-9.65283954218
106.670787759943.19155841876-1.721360190448.5706174698-0.996585939725.221920419320.102694250195-0.7176461305040.5831936371520.829312137525-0.04464575134570.768690431518-0.263828849017-0.821288086631-0.1705041441230.3393543709160.1013640585590.06303719910220.742166709105-0.1371717078230.357409725547-28.398172366427.860778910910.974383461
112.22922019119-0.3420509758590.5095788538023.209924115211.039702257242.91384659628-0.148763855644-0.7337745491110.3910321914850.3897171051550.0165951457328-0.147187617829-0.391149634042-0.2537790849970.05658514971430.186750529336-0.0009761415436730.04240853209880.458630939188-0.1630442534980.362507031411-23.764596928230.03367199324.53663532853
126.880329390612.915279428112.566987693817.334687833781.462692413766.976022161980.3020727866740.505126910425-0.4738738539190.0607020438168-0.4290779374411.396808777370.69329581591-0.9731964552470.1054635998530.319791373653-0.0616815809621-0.003316181311370.584397158033-0.2106816439070.592514781322-41.96967220739.4721670133-19.8638094509
137.43561081832-5.150134516530.2020916092878.060320390193.50855315063.595357101690.4762998713010.377225163326-0.413487339528-0.988773288705-0.299482485880.4240681917950.559208852052-0.387823451977-0.1396614323010.454334591337-0.1711897703280.05266721810990.535027079472-0.131355387820.396259419515-38.810650137312.8155891622-14.4160878195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 46 )
2X-RAY DIFFRACTION2chain 'B' and (resid 47 through 61 )
3X-RAY DIFFRACTION3chain 'B' and (resid 62 through 178 )
4X-RAY DIFFRACTION4chain 'B' and (resid 179 through 198 )
5X-RAY DIFFRACTION5chain 'B' and (resid 199 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 11 )
7X-RAY DIFFRACTION7chain 'A' and (resid 12 through 46 )
8X-RAY DIFFRACTION8chain 'A' and (resid 47 through 61 )
9X-RAY DIFFRACTION9chain 'A' and (resid 62 through 124 )
10X-RAY DIFFRACTION10chain 'A' and (resid 125 through 148 )
11X-RAY DIFFRACTION11chain 'A' and (resid 149 through 178 )
12X-RAY DIFFRACTION12chain 'A' and (resid 179 through 197 )
13X-RAY DIFFRACTION13chain 'A' and (resid 198 through 223 )

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