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- PDB-2rhm: Crystal structure of a putative kinase (caur_3907) from chlorofle... -

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Basic information

Entry
Database: PDB / ID: 2rhm
TitleCrystal structure of a putative kinase (caur_3907) from chloroflexus aurantiacus j-10-fl at 1.70 A resolution
ComponentsPutative kinase
KeywordsUNKNOWN FUNCTION / P-loop containing nucleoside triphosphate hydrolases fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / BENZOIC ACID / ATP-binding protein / :
Function and homology information
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative kinase (ZP_00765535.1) from Chloroflexus aurantiacus J-10-fl at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative kinase
B: Putative kinase
C: Putative kinase
D: Putative kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,72113
Polymers86,0594
Non-polymers6629
Water11,007611
1
A: Putative kinase
B: Putative kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3146
Polymers43,0292
Non-polymers2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
MethodPISA
2
C: Putative kinase
D: Putative kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4067
Polymers43,0292
Non-polymers3775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.930, 76.790, 129.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Putative kinase


Mass: 21514.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: ZP_00765535.1, CaurDRAFT_1197 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3E6M1, UniProt: A9WDG5*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. REMARK 999

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.141.44TWO CRYSTALS WERE USED IN THE SOLUTION OF THIS STRUCTURE, ONE FOR PHASING AND ONE FOR REFINEMENT. THE 1.96 A MAD PHASES WERE USED AS RESTRAINTS DURING THE REFINEMENT OF 1.7 A REFINEMENT DATA SET.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop6.5NANODROP, 0.2M MgCl2, 10.0% PEG 3000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting dropNANODROP, 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG 8000, no buffer, no pH, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.99187
SYNCHROTRONAPS 23-ID-D20.97957, 0.95373
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991871
20.979571
30.953731
ReflectionResolution: 1.7→29.761 Å / Num. obs: 73034 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 5.17 % / Biso Wilson estimate: 33.512 Å2 / Rmerge(I) obs: 0.0667 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.7-1.84.020.62782.4811562192.7
1.8-1.854.080.45223.424911192.6
1.85-1.94.050.36944.234359191.9
1.9-1.953.970.29345.623901191.3
1.95-2.054.10.19757.166779192
2.05-2.154.020.14959.325527191
2.15-2.254.020.114211.344614191.3
2.25-2.354.030.09512.923852190.9
2.35-2.54.410.0915.094670191.2
2.5-2.656.140.118317.53707190.9
2.65-2.857.290.101120.713774190.5
2.85-3.158.070.078824.634013189.9
3.15-3.68.050.060228.93762189.3
3.6-4.557.930.0531.893846187.3
4.55-29.7617.410.047132.463757183.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.761 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.197 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.12
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. FOUR CHLORIDE ANIONS, TWO BENZOIC ACID AND THREE GLYCEROL MOLECULES ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3714 5.1 %RANDOM
Rwork0.181 ---
obs0.183 72956 90.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5571 0 40 611 6222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225883
X-RAY DIFFRACTIONr_bond_other_d0.0010.025602
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9768017
X-RAY DIFFRACTIONr_angle_other_deg0.751312920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6715771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.922.689212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40315971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.171549
X-RAY DIFFRACTIONr_chiral_restr0.0670.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
X-RAY DIFFRACTIONr_nbd_refined0.2240.31360
X-RAY DIFFRACTIONr_nbd_other0.170.35763
X-RAY DIFFRACTIONr_nbtor_refined0.1740.52959
X-RAY DIFFRACTIONr_nbtor_other0.0840.53446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5774
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1260.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.333
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.3110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.523
X-RAY DIFFRACTIONr_mcbond_it1.533908
X-RAY DIFFRACTIONr_mcbond_other0.33531543
X-RAY DIFFRACTIONr_mcangle_it2.19956169
X-RAY DIFFRACTIONr_scbond_it3.82682178
X-RAY DIFFRACTIONr_scangle_it5.441111848
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 279 -
Rwork0.254 5113 -
all-5392 -
obs--91.51 %
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)
11.23250.54150.69911.66680.93242.2933-0.0682-0.10720.1893-0.0490.05820.0018-0.22960.19140.0099-0.0867-0.09290.0150.0152-0.0108-0.010433.447837.21124.6211
21.8417-0.0185-0.09720.4067-0.26181.2706-0.00520.1873-0.04-0.039-0.02250.01290.01760.01110.0277-0.0761-0.0210.0104-0.04820.0038-0.066217.478919.81787.0374
31.8075-0.4148-0.44371.1767-0.23031.7658-0.0566-0.1394-0.06790.49930.13270.2965-0.4035-0.1676-0.07610.1820.11020.137-0.08510.041-0.001219.360454.5156-7.266
40.3241-0.0732-0.04421.8577-0.15960.9354-0.00240.0307-0.04140.0542-0.0153-0.0286-0.02990.04830.0177-0.10380.0197-0.0041-0.06380.0057-0.048937.187640.6856-26.2726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1891 - 190
2X-RAY DIFFRACTION2BB0 - 1871 - 188
3X-RAY DIFFRACTION3CC1 - 1892 - 190
4X-RAY DIFFRACTION4DD2 - 1863 - 187

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