HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 30-JUN-09 2KL6 TITLE SOLUTION NMR STRUCTURE OF THE CARDB DOMAIN OF PF1109 FROM PYROCOCCUS TITLE 2 FURIOSUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET PFR193A COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 436-540; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: PF1109; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PFR193A-436-540-21.36 KEYWDS SOLUTION NMR STRUCTURE, CARDB DOMAIN, PFAM 07705, NESG, PSI-2, KEYWDS 2 STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,D.LEE,C.CICCOSANTI,K.HAMILTON,R.NAIR,B.ROST,T.B.ACTON, AUTHOR 2 R.XIAO,G.V.T.SWAPNA,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 5 08-MAY-24 2KL6 1 REMARK REVDAT 4 14-JUN-23 2KL6 1 REMARK REVDAT 3 13-OCT-21 2KL6 1 SEQADV REVDAT 2 26-FEB-20 2KL6 1 REMARK SEQADV REVDAT 1 25-AUG-09 2KL6 0 JRNL AUTH J.M.ARAMINI,D.LEE,C.CICCOSANTI,K.HAMILTON,R.NAIR,B.ROST, JRNL AUTH 2 T.B.ACTON,R.XIAO,G.V.T.SWAPNA,J.K.EVERETT,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE CARDB DOMAIN OF PF1109 FROM JRNL TITL 2 PYROCOCCUS FURIOSUS. NORTHEAST STRUCTURAL GENOMICS JRNL TITL 3 CONSORTIUM TARGET PFR193A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CNS 1.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 2722 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS AND 166 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND REMARK 3 CONSTRAINTS (26.7 CONSTRAINTS PER RESIDUE, 11.5 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 108 BY PSVS REMARK 3 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET REMARK 3 FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. REMARK 3 AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. REMARK 3 BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM REMARK 3 TALOSPLUS. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO REMARK 3 108, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] REMARK 3 COMPRISE: 2-107: (A) RMSD (ORDERED RESIDUES): BB, 0.4, HEAVY REMARK 3 ATOM, 0.6. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: REMARK 3 MOST FAVORED, 93.3%, ADDITIONALLY ALLOWED, 6.5%, GENEROUSLY REMARK 3 ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED REMARK 3 RESIDUES (RAW/Z-): PHI-PSI, -0.42/-1.34, ALL, -0.27/-1.60. (D) REMARK 3 MOLPROBITY CLASH SCORE (RAW/Z-): 15.99/-1.22 (E) RPF SCORES FOR REMARK 3 GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-108): RECALL, 0.963, REMARK 3 PRECISION, 0.951, F-MEASURE, 0.957, DP-SCORE, 0.861. (F) NUMBER REMARK 3 OF CLOSE CONTACTS PER 20 MODELS: 4. REMARK 4 REMARK 4 2KL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101257. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.65 MM [U-100% 13C; U-100% 15N] REMARK 210 PFR193A, 20 MM MES, 200 MM REMARK 210 SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 0.02 % REMARK 210 SODIUM AZIDE, 50 UM DSS, 90% H2O/ REMARK 210 10% D2O; 0.43 MM [U-5% 13C; U- REMARK 210 100% 15N] PFR193A, 20 MM MES, REMARK 210 200 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 50 UM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C HSQC HIGH REMARK 210 RESOLUTION (L/V METHYL REMARK 210 STEREOASSIGNMENT); 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HN(CO)CA; 3D HNCA; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 3D HNHA; REMARK 210 2D 1H-15N HETNOE; 1D 15N T1 AND REMARK 210 T2 REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, NMRPIPE 2.3, SPARKY REMARK 210 3.112, PINE 1.0, CYANA 3.0, REMARK 210 AUTOSTRUCTURE 2.2.1, PSVS 1.3, REMARK 210 MOLPROBITY 3.15, PDBSTAT 5.1, REMARK 210 TALOS PLUS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE PROTEIN IS PREDOMINANTLY MONOMERIC BY GEL FILTRATION REMARK 210 CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 REMARK 210 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE REMARK 210 NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN REMARK 210 ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. REMARK 210 ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CROYOPROBE. REMARK 210 BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. COMPLETENESS OF NMR REMARK 210 ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.7%, SIDE REMARK 210 CHAIN, 99.0%, AROMATICS, 98.8%, STEREOSPECIFIC METHYL, 88.5%, REMARK 210 STEREOSPECIFIC SIDE CHAIN NH2: 100%. THE C-TERMINAL HIS TAG REMARK 210 RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE REMARK 210 STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS REMARK 210 DEPOSITION. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 HIS A 548 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ASP A 439 81.59 -153.58 REMARK 500 1 PRO A 493 95.38 -59.24 REMARK 500 2 ASP A 439 83.66 -151.60 REMARK 500 3 ASP A 439 86.79 -155.73 REMARK 500 3 ASN A 521 82.11 62.59 REMARK 500 4 PRO A 493 108.75 -57.56 REMARK 500 4 ASN A 521 78.94 65.52 REMARK 500 5 ASN A 453 16.57 59.40 REMARK 500 5 PRO A 493 107.68 -53.53 REMARK 500 6 ASP A 439 86.84 -153.70 REMARK 500 6 PRO A 493 105.72 -59.95 REMARK 500 7 ASP A 439 81.42 -153.94 REMARK 500 7 PRO A 493 106.43 -58.44 REMARK 500 7 ASN A 521 72.14 55.97 REMARK 500 8 ASP A 439 87.59 -153.84 REMARK 500 9 ASP A 439 86.81 -161.25 REMARK 500 9 PRO A 493 103.50 -58.63 REMARK 500 9 ASP A 518 64.89 38.74 REMARK 500 10 ASP A 439 87.99 -153.29 REMARK 500 10 ASP A 518 60.97 36.28 REMARK 500 10 ASN A 521 74.15 51.04 REMARK 500 12 ASP A 518 66.59 38.96 REMARK 500 14 ASP A 439 78.20 -152.87 REMARK 500 14 PRO A 493 105.84 -57.97 REMARK 500 14 ASN A 521 70.22 52.02 REMARK 500 15 ASP A 518 70.41 43.80 REMARK 500 17 ASP A 518 71.58 35.46 REMARK 500 17 ASN A 521 79.36 51.51 REMARK 500 18 PRO A 493 99.53 -61.90 REMARK 500 18 ASN A 521 71.92 59.31 REMARK 500 19 ASP A 439 80.29 -154.06 REMARK 500 20 ASP A 439 81.64 -154.85 REMARK 500 20 PRO A 493 97.03 -60.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16385 RELATED DB: BMRB REMARK 900 RELATED ID: PFR193A RELATED DB: TARGETDB DBREF 2KL6 A 436 540 UNP Q8U1U6 Q8U1U6_PYRFU 436 540 SEQADV 2KL6 MET A 435 UNP Q8U1U6 INITIATING METHIONINE SEQADV 2KL6 SER A 502 UNP Q8U1U6 ASN 502 ENGINEERED MUTATION SEQADV 2KL6 LEU A 541 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 GLU A 542 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 HIS A 543 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 HIS A 544 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 HIS A 545 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 HIS A 546 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 HIS A 547 UNP Q8U1U6 EXPRESSION TAG SEQADV 2KL6 HIS A 548 UNP Q8U1U6 EXPRESSION TAG SEQRES 1 A 114 MET GLU PHE PRO ASP LEU THR VAL GLU ILE LYS GLY PRO SEQRES 2 A 114 ASP VAL VAL GLY VAL ASN LYS LEU ALA GLU TYR GLU VAL SEQRES 3 A 114 HIS VAL LYS ASN LEU GLY GLY ILE GLY VAL PRO SER THR SEQRES 4 A 114 LYS VAL ARG VAL TYR ILE ASN GLY THR LEU TYR LYS ASN SEQRES 5 A 114 TRP THR VAL SER LEU GLY PRO LYS GLU GLU LYS VAL LEU SEQRES 6 A 114 THR PHE SER TRP THR PRO THR GLN GLU GLY MET TYR ARG SEQRES 7 A 114 ILE ASN ALA THR VAL ASP GLU GLU ASN THR VAL VAL GLU SEQRES 8 A 114 LEU ASN GLU ASN ASN ASN VAL ALA THR PHE ASP VAL SER SEQRES 9 A 114 VAL VAL LEU GLU HIS HIS HIS HIS HIS HIS SHEET 1 A 3 LEU A 440 LYS A 445 0 SHEET 2 A 3 ALA A 456 ASN A 464 -1 O GLU A 459 N LYS A 445 SHEET 3 A 3 GLU A 496 TRP A 503 -1 O LEU A 499 N VAL A 460 SHEET 1 B 5 VAL A 449 GLY A 451 0 SHEET 2 B 5 VAL A 532 VAL A 540 1 O SER A 538 N VAL A 450 SHEET 3 B 5 GLY A 509 VAL A 517 -1 N ILE A 513 O PHE A 535 SHEET 4 B 5 VAL A 470 ILE A 479 -1 N TYR A 478 O ASN A 514 SHEET 5 B 5 THR A 482 LEU A 491 -1 O THR A 482 N ILE A 479 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1