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- PDB-5i1v: Crystal structure of CrmK, a flavoenzyme involved in the shunt pr... -

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Basic information

Entry
Database: PDB / ID: 5i1v
TitleCrystal structure of CrmK, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin biosynthesis
ComponentsCrmK
KeywordsOXIDOREDUCTASE / flavoenzyme / oxidase / covalently bound FAD
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / CrmK
Similarity search - Component
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsPicard, M.-E. / Barma, J. / Shi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: to be published
Title: Biochemical and structural insights into flavoenzyme CrmK reveals a shunt product recycling mechanism in caerulomycin biosynthesis
Authors: Zhu, Y. / Picard, M.-E. / Mei, X. / Zhang, Q. / Barma, J. / Murphy Despres, X. / Couture, M. / Zhu, W. / Zhang, C. / Shi, R.
History
DepositionFeb 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CrmK
B: CrmK
C: CrmK
D: CrmK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,2858
Polymers221,1434
Non-polymers3,1424
Water24,9691386
1
A: CrmK
B: CrmK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1434
Polymers110,5712
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-34 kcal/mol
Surface area34150 Å2
MethodPISA
2
C: CrmK
D: CrmK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1434
Polymers110,5712
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-34 kcal/mol
Surface area34130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.630, 95.730, 98.440
Angle α, β, γ (deg.)95.180, 96.980, 104.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CrmK


Mass: 55285.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoalloteichus sp. WH1-2216-6 (bacteria)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8Y6P5
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1386 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 0.96 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→96.94 Å / Num. obs: 184445 / % possible obs: 95.9 % / Redundancy: 4 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.993 / Rsym value: 0.118 / Net I/av σ(I): 4.864 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.84-1.943.90.8280.8194.7
1.94-2.0640.5241.2195.1
2.06-2.240.322.1195.4
2.2-2.3840.233195.8
2.38-2.640.1574.5196.1
2.6-2.9140.1116.3196.5
2.91-3.3640.0887.4196.8
3.36-4.1140.0758.8197.1
4.11-5.8240.0669.8197.5
5.82-48.4740.06110197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y08

2y08


Resolution: 1.84→96.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.269 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.115
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 9296 5 %RANDOM
Rwork0.1608 ---
obs0.1625 175148 95.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 30.26 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å21.45 Å20.21 Å2
2---0.29 Å20.02 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 1.84→96.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15553 0 212 1386 17151
Biso mean--19.85 37.52 -
Num. residues----1991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916324
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214812
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.95422371
X-RAY DIFFRACTIONr_angle_other_deg0.894333923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27152013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74322.356781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.646152301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.46515161
X-RAY DIFFRACTIONr_chiral_restr0.1020.22370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023991
X-RAY DIFFRACTIONr_mcbond_it1.9182.3798005
X-RAY DIFFRACTIONr_mcbond_other1.9132.3788004
X-RAY DIFFRACTIONr_mcangle_it2.7633.55710009
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 651 -
Rwork0.27 12728 -
all-13379 -
obs--94.42 %
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)
10.1234-0.0540.00180.4072-0.07920.2407-0.0407-0.01050.01180.0529-0.0139-0.08380.0280.00040.05470.0240.0002-0.00880.00930.01210.0408-6.496826.40276.8665
20.2053-0.0298-0.15680.10430.02820.39730.0269-0.0050.0172-0.01-0.0103-0.0102-0.04630.0223-0.01650.0111-0.0091-0.00380.01460.00720.0292-11.955856.051758.596
30.1753-0.06460.02920.12350.06590.19970.03360.0029-0.006-0.0127-0.0098-0.0045-0.00460.0051-0.02380.0098-0.0089-0.00010.0283-0.0010.0231-12.1676-12.932497.5052
40.2244-0.0082-0.04430.27220.0060.18970.0070.00110.0080.02820.00620.01890.00620.0239-0.01320.0094-0.0065-0.00370.02320.0010.0108-17.3549-15.3776132.3747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 600
2X-RAY DIFFRACTION2B3 - 600
3X-RAY DIFFRACTION3C4 - 600
4X-RAY DIFFRACTION4D3 - 600

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