HEADER LIGASE 05-JUL-16 5LG0 TITLE SOLUTION NMR STRUCTURE OF TRYPTOPHAN TO ALANINE MUTANT OF ARKADIA RING TITLE 2 DOMAIN. CAVEAT 5LG0 LYS A 2 HAS WRONG CHIRALITY AT ATOM CA THR A 9 HAS WRONG CAVEAT 2 5LG0 CHIRALITY AT ATOM CB PRO A 66 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 5LG0 CA SER A 69 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE ARKADIA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RING FINGER PROTEIN 111; COMPND 5 EC: 6.3.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RNF111; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-47-1 KEYWDS ARKADIA, RNF111, E3 UBIQUITIN LIGASE, RING DOMAIN, TRYPTOPHAN, TGF-B, KEYWDS 2 UBCH5B E2 ENZYME, LIGASE EXPDTA SOLUTION NMR NUMMDL 31 AUTHOR M.BIRKOU,C.T.CHASAPIS,A.K.LOUTSIDOU,D.BENTROP,M.LELLI,T.HERRMANN, AUTHOR 2 V.EPISKOPOU,G.A.SPYROULIAS REVDAT 5 14-JUN-23 5LG0 1 REMARK REVDAT 4 08-MAY-19 5LG0 1 REMARK REVDAT 3 26-JUL-17 5LG0 1 REVDAT 2 05-JUL-17 5LG0 1 JRNL REMARK REVDAT 1 28-JUN-17 5LG0 0 JRNL AUTH M.BIRKOU,C.T.CHASAPIS,K.D.MAROUSIS,A.K.LOUTSIDOU,D.BENTROP, JRNL AUTH 2 M.LELLI,T.HERRMANN,J.M.CARTHY,V.EPISKOPOU,G.A.SPYROULIAS JRNL TITL A RESIDUE SPECIFIC INSIGHT INTO THE ARKADIA E3 UBIQUITIN JRNL TITL 2 LIGASE ACTIVITY AND CONFORMATIONAL PLASTICITY. JRNL REF J. MOL. BIOL. V. 429 2373 2017 JRNL REFN ESSN 1089-8638 JRNL PMID 28647409 JRNL DOI 10.1016/J.JMB.2017.06.012 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000518. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-99% 15N] ARKADIA RING REMARK 210 W972A, 50 MM POTASSIUM PHOSPHATE, REMARK 210 2 MM DSS, 90% H2O/10% D2O; 0.6 REMARK 210 MM [U-99% 13C; U-99% 15N] REMARK 210 ARKADIA RING W972A, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 2 MM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNHA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 HCCH-TOCSY; 2D 1H-13C HSQC; 4D REMARK 210 APSY-HACANH; 5D APSY-CBCACONH; REMARK 210 5D APSY-HACACONH REMARK 210 SPECTROMETER FIELD STRENGTH : 1000 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : SB AVANCEIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8.4, UNIO 10 REMARK 210 METHOD USED : MOLECULAR MECHANICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 31 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 GLN A 3 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 1 ILE A 56 CB - CG1 - CD1 ANGL. DEV. = 23.9 DEGREES REMARK 500 4 CYS A 57 CB - CA - C ANGL. DEV. = 7.8 DEGREES REMARK 500 26 CYS A 57 CB - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 2 -157.84 -118.26 REMARK 500 1 GLN A 3 -136.30 55.71 REMARK 500 1 GLU A 6 -127.27 39.42 REMARK 500 1 GLU A 7 117.04 148.14 REMARK 500 1 GLU A 10 -178.37 62.85 REMARK 500 1 ASP A 12 96.07 72.63 REMARK 500 1 GLU A 14 -57.15 -142.16 REMARK 500 1 MET A 36 60.73 22.15 REMARK 500 1 ARG A 58 -22.12 72.57 REMARK 500 1 GLU A 62 86.17 -56.57 REMARK 500 1 PRO A 66 -8.35 85.52 REMARK 500 1 SER A 67 -144.61 -154.09 REMARK 500 2 GLU A 6 -50.52 -168.28 REMARK 500 2 GLU A 7 -9.66 68.66 REMARK 500 2 LEU A 24 -156.54 -94.97 REMARK 500 2 ASP A 29 98.65 -68.98 REMARK 500 2 CYS A 35 43.27 -87.98 REMARK 500 2 MET A 36 63.18 32.69 REMARK 500 2 CYS A 57 -38.20 -172.17 REMARK 500 2 ALA A 63 83.50 -150.75 REMARK 500 2 GLN A 64 145.14 78.23 REMARK 500 3 GLN A 3 -51.88 -166.35 REMARK 500 3 ASP A 4 -164.74 64.40 REMARK 500 3 ASP A 12 145.39 67.55 REMARK 500 3 THR A 13 5.23 -151.15 REMARK 500 3 LEU A 24 -157.10 -96.95 REMARK 500 3 CYS A 35 6.69 -64.45 REMARK 500 3 GLN A 41 21.96 -70.19 REMARK 500 3 VAL A 42 -62.56 -127.80 REMARK 500 3 ILE A 56 61.31 35.44 REMARK 500 3 CYS A 57 -60.55 -166.28 REMARK 500 3 GLN A 64 129.00 114.10 REMARK 500 3 SER A 67 -91.85 -161.57 REMARK 500 4 GLU A 7 -103.51 -144.49 REMARK 500 4 THR A 13 21.54 -145.32 REMARK 500 4 GLU A 15 77.36 -106.27 REMARK 500 4 LEU A 24 -147.86 -101.37 REMARK 500 4 VAL A 30 -169.50 -126.04 REMARK 500 4 CYS A 35 34.49 -81.21 REMARK 500 4 LYS A 52 44.64 -82.65 REMARK 500 4 ILE A 56 -54.59 -157.49 REMARK 500 4 CYS A 57 -140.22 -113.42 REMARK 500 4 ARG A 58 28.99 -148.89 REMARK 500 4 GLU A 62 92.09 -60.55 REMARK 500 4 ALA A 63 45.96 -152.03 REMARK 500 4 LEU A 65 86.46 46.45 REMARK 500 4 GLU A 68 111.19 110.49 REMARK 500 5 LYS A 2 175.81 55.09 REMARK 500 5 GLN A 3 47.08 -172.95 REMARK 500 5 ASP A 12 89.92 -160.74 REMARK 500 REMARK 500 THIS ENTRY HAS 320 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 1 LYS A 2 1 106.91 REMARK 500 GLN A 3 ASP A 4 1 -138.63 REMARK 500 ASP A 4 GLY A 5 1 146.29 REMARK 500 GLU A 6 GLU A 7 1 -111.21 REMARK 500 GLU A 10 GLU A 11 1 -137.17 REMARK 500 CYS A 35 MET A 36 23 144.47 REMARK 500 ILE A 56 CYS A 57 27 147.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 22 ARG A 31 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 17 SG REMARK 620 2 CYS A 20 SG 118.3 REMARK 620 3 HIS A 40 ND1 108.0 116.6 REMARK 620 4 CYS A 43 SG 117.6 86.1 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 35 O REMARK 620 2 CYS A 35 SG 88.9 REMARK 620 3 HIS A 37 ND1 96.1 119.6 REMARK 620 4 CYS A 54 SG 130.4 114.6 106.9 REMARK 620 5 CYS A 57 SG 162.9 75.4 97.5 54.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KIZ RELATED DB: PDB REMARK 900 ARKADIA WILD-TYPE RING DOMAIN (69A.A.) REMARK 900 RELATED ID: 25249 RELATED DB: BMRB REMARK 900 RELATED ID: 5LG7 RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF TRYPTOPHAN TO ARGININE MUTANT OF ARKADIA REMARK 900 RING DOMAIN DBREF 5LG0 A 2 69 UNP Q6ZNA4 RN111_HUMAN 927 994 SEQADV 5LG0 MET A 1 UNP Q6ZNA4 INITIATING METHIONINE SEQADV 5LG0 ALA A 47 UNP Q6ZNA4 TRP 972 ENGINEERED MUTATION SEQRES 1 A 69 MET LYS GLN ASP GLY GLU GLU GLY THR GLU GLU ASP THR SEQRES 2 A 69 GLU GLU LYS CYS THR ILE CYS LEU SER ILE LEU GLU GLU SEQRES 3 A 69 GLY GLU ASP VAL ARG ARG LEU PRO CYS MET HIS LEU PHE SEQRES 4 A 69 HIS GLN VAL CYS VAL ASP GLN ALA LEU ILE THR ASN LYS SEQRES 5 A 69 LYS CYS PRO ILE CYS ARG VAL ASP ILE GLU ALA GLN LEU SEQRES 6 A 69 PRO SER GLU SER HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 GLN A 41 ASN A 51 1 11 SHEET 1 AA1 2 LYS A 16 CYS A 17 0 SHEET 2 AA1 2 SER A 22 ILE A 23 -1 O SER A 22 N CYS A 17 SHEET 1 AA2 2 VAL A 30 LEU A 33 0 SHEET 2 AA2 2 HIS A 37 HIS A 40 -1 O PHE A 39 N ARG A 31 SSBOND 1 CYS A 20 CYS A 43 1555 1555 2.84 SSBOND 2 CYS A 35 CYS A 57 1555 1555 2.68 SSBOND 3 CYS A 54 CYS A 57 1555 1555 2.00 LINK SG CYS A 17 ZN ZN A 101 1555 1555 2.12 LINK SG CYS A 20 ZN ZN A 101 1555 1555 2.07 LINK O CYS A 35 ZN ZN A 102 1555 1555 1.77 LINK SG CYS A 35 ZN ZN A 102 1555 1555 2.20 LINK ND1 HIS A 37 ZN ZN A 102 1555 1555 2.12 LINK ND1 HIS A 40 ZN ZN A 101 1555 1555 2.09 LINK SG CYS A 43 ZN ZN A 101 1555 1555 2.09 LINK SG CYS A 54 ZN ZN A 102 1555 1555 2.20 LINK SG CYS A 57 ZN ZN A 102 1555 1555 2.20 CISPEP 1 LYS A 2 GLN A 3 1 19.25 CISPEP 2 THR A 9 GLU A 10 1 4.76 CISPEP 3 LEU A 65 PRO A 66 1 19.58 SITE 1 AC1 4 CYS A 17 CYS A 20 HIS A 40 CYS A 43 SITE 1 AC2 4 CYS A 35 HIS A 37 CYS A 54 CYS A 57 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