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- PDB-9jn6: Crystal structure of KtzT-C197A in complex with HEME and product -

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Basic information

Entry
Database: PDB / ID: 9jn6
TitleCrystal structure of KtzT-C197A in complex with HEME and product
ComponentsFMN-binding protein
KeywordsOXIDOREDUCTASE / Heme-dependent piperazate synthase
Function / homologyTranscriptional regulator PAI 2-type / Putative FMN-binding domain / FMN-binding split barrel / : / PROTOPORPHYRIN IX CONTAINING FE / FMN-binding protein
Function and homology information
Biological speciesKutzneria sp. 744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLi, Y.L. / Yang, Y.Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911400 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural Insights into the N-N Bond-Formation Mechanism of the Heme-Dependent Piperazate Synthase KtzT
Authors: Yang, Y. / Li, Y. / Yao, L. / Dai, K. / Fu, X. / Ge, A. / Huang, J.W. / Guo, R.T. / Chen, C.C.
History
DepositionSep 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: FMN-binding protein
C: FMN-binding protein
D: FMN-binding protein
A: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,85411
Polymers92,9974
Non-polymers2,8567
Water15,331851
1
B: FMN-binding protein
C: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8625
Polymers46,4992
Non-polymers1,3633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-75 kcal/mol
Surface area17650 Å2
MethodPISA
2
D: FMN-binding protein
A: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9926
Polymers46,4992
Non-polymers1,4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-79 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.878, 101.613, 111.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FMN-binding protein / Regulator


Mass: 23249.340 Da / Num. of mol.: 4 / Mutation: C197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kutzneria sp. 744 (bacteria) / Gene: KUTG_08928 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8CF72
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-A1ECN / (3~{S})-1,2-diazinane-3-carboxylic acid / (S)-Hexahydropyridazine-3-carboxylic acid / S-Piperazic acid / (3S)-piperazate / (3S)-Pyridazin-3-carboxylate


Type: peptide-like / Mass: 130.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.1 M ammonium acetate, 0.1 M Tris pH 8.0, 1.0 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.72→29.24 Å / Num. obs: 109356 / % possible obs: 97.6 % / Redundancy: 7.5 % / CC1/2: 0.999 / Net I/σ(I): 13.95
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.59 / Num. unique obs: 17022 / CC1/2: 0.95 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→29.24 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.254 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22196 1999 1.8 %RANDOM
Rwork0.18702 ---
obs0.18766 107504 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-0 Å2
2---1.68 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.72→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6443 0 199 851 7493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136846
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176294
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.6959398
X-RAY DIFFRACTIONr_angle_other_deg1.5611.60414409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38219.13368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76515929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5631576
X-RAY DIFFRACTIONr_chiral_restr0.0860.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027924
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3392.3913413
X-RAY DIFFRACTIONr_mcbond_other2.3392.3923414
X-RAY DIFFRACTIONr_mcangle_it3.4993.5734254
X-RAY DIFFRACTIONr_mcangle_other3.53.5734255
X-RAY DIFFRACTIONr_scbond_it3.3482.6723433
X-RAY DIFFRACTIONr_scbond_other3.3482.6723433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0973.8625145
X-RAY DIFFRACTIONr_long_range_B_refined6.8929.148044
X-RAY DIFFRACTIONr_long_range_B_other6.8929.1438045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.761 Å
RfactorNum. reflection% reflection
Rfree0.308 138 -
Rwork0.261 7434 -
obs--93.9 %

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