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- PDB-9vyc: The crystal structure of PaiB from Bacillus stearothermophilus bo... -

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Basic information

Entry
Database: PDB / ID: 9vyc
TitleThe crystal structure of PaiB from Bacillus stearothermophilus bound to HEM
ComponentsPaiB
KeywordsTRANSCRIPTION / Transcriptional repressor of sporulation and degradative enzymes production
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesGeobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42122719099 Å
AuthorsZhang, Z.M. / Huang, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2025
Title: Structural insights into heme-iron dependent N-N bond formation enzyme LnzB.
Authors: Huang, H. / Wang, L. / Chen, P. / Yang, T. / Zhu, C. / Li, S. / Zhou, Y. / Tan, Y. / Li, Z. / Zhang, H. / Chen, J. / Zhang, Z.M.
History
DepositionJul 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PaiB
B: PaiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2174
Polymers46,9842
Non-polymers1,2332
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-81 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.442, 89.906, 62.586
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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
11TYRTYRPROPROchain 'A'AA2 - 42 - 4
12ALAALALYSLYSchain 'A'AA8 - 1988 - 198
23TYRTYRPROPROchain 'B'BB2 - 42 - 4
24ALAALALYSLYSchain 'B'BB8 - 1988 - 198

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Components

#1: Protein PaiB


Mass: 23491.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria)
Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium fluoride,20% peg 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.41→44.954 Å / Num. obs: 16974 / % possible obs: 99.94 % / Redundancy: 11.1 % / CC1/2: 0.877 / Net I/σ(I): 2.4
Reflection shellResolution: 2.42→2.51 Å / Num. unique obs: 16974 / CC1/2: 0.877

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42122719099→44.953 Å / SU ML: 0.257064184062 / Cross valid method: NONE / σ(F): 1.33461764965 / Phase error: 28.3072577432
RfactorNum. reflection% reflection
Rfree0.251688683564 1682 10.03400346 %
Rwork0.210546279635 15081 -
obs0.214702397439 16763 98.6116830402 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.7358174092 Å2
Refinement stepCycle: LAST / Resolution: 2.42122719099→44.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 86 113 3360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004675592838233338
X-RAY DIFFRACTIONf_angle_d1.109595658124548
X-RAY DIFFRACTIONf_chiral_restr0.0433232840897467
X-RAY DIFFRACTIONf_plane_restr0.00494348823435585
X-RAY DIFFRACTIONf_dihedral_angle_d17.90210668221222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.422-2.49250.3450028408451370.2832198882611239X-RAY DIFFRACTION99.064074874
2.4925-2.57290.3247357737711400.2686159796891255X-RAY DIFFRACTION99.5717344754
2.5729-2.66490.273407808351380.2658032731231239X-RAY DIFFRACTION99.6382054993
2.6649-2.77150.3200602828041380.2481220292781239X-RAY DIFFRACTION99.7826086957
2.7715-2.89770.2595640688911410.2382467881031267X-RAY DIFFRACTION99.716713881
2.8977-3.05040.271266936191370.2432462285711241X-RAY DIFFRACTION99.3511175198
3.0504-3.24150.3006133836911400.2295421175511250X-RAY DIFFRACTION98.6515259049
3.2415-3.49160.2695208615231370.2218345811431225X-RAY DIFFRACTION96.2544169611
3.4916-3.84290.2591935476671390.2092152009051241X-RAY DIFFRACTION97.3888496824
3.8429-4.39850.1947519245491420.1802457014071266X-RAY DIFFRACTION98.8070175439
4.3985-5.54010.2269297648171420.1759893934051287X-RAY DIFFRACTION98.1456043956
5.5401-44.950.2216485794121510.1823703227331332X-RAY DIFFRACTION97.3097112861
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)
10.435580387683-0.729015968414-0.5666505947611.967007042520.7873631764520.858035528533-0.0728150980237-0.04599593884790.05316197486030.09772764529140.102294406146-0.1938362224220.06297376448590.073119192875-0.0002304503677090.26055594857-0.0184296944518-0.05134877111460.272146181362-0.004932209040410.2626259799032.995313786436.65568990678-22.0186822393
20.213474570569-0.1579693312690.3736280614561.36239267469-0.575382140140.6417932736660.153600161863-0.01187050931870.161456383674-0.1631399127640.00824565827867-0.147754557383-0.1507883340080.0302411158892-0.0001186164026920.463588249701-0.00919061235719-0.006745373318740.327390716099-0.01375801850990.340088768184.7177373210110.0214941571-32.4813226563
30.2731328971250.335032223133-0.06673284064311.27859411629-0.2532945043761.20515788255-0.0263205636349-0.06491696028750.0655052685156-0.381902441045-0.01786652872570.1913005550080.4675252937-0.233988313782-0.09807212966630.282155096791-0.0341346424759-0.07417598165580.282565385914-0.03858024831360.321925528557-2.13514012492-8.27613128263-32.8691047647
40.2441656645010.2369038721460.2240695445021.69073886343-0.9325088990460.8159535044980.02827831784950.0808634513843-0.128285455948-0.611084827464-0.08796456599340.2241895506750.360864758169-0.0737473933769-0.0004817063908710.3959811962760.00846537919058-0.0796122909450.335004540711-0.01435815440820.288757347862-3.98337848124-2.72402171911-37.5720012953
50.209638733298-0.2670915402220.03859094477550.5255011083320.2895268382840.5554726505570.125251674075-0.389206164171-0.139091666676-0.49305290595-0.1730010581460.670745015172-0.548994275391-0.5306890938450.002616983505730.4760994333070.0609698883762-0.02477303400850.578917468172-0.004829757593470.496862419583-16.522327970516.4163392059-27.3563582569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 199 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 75 )
4X-RAY DIFFRACTION4chain 'B' and (resid 76 through 165 )
5X-RAY DIFFRACTION5chain 'B' and (resid 166 through 200 )

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