HEADER ANTIVIRAL PROTEIN 07-DEC-06 2JMV TITLE SOLUTION STRUCTURE OF SCYTOVIRIN REFINED AGAINST RESIDUAL DIPOLAR TITLE 2 COUPLINGS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCYTOVIRIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SVN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCYTONEMA VARIUM; SOURCE 3 ORGANISM_TAXID: 423208; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET32 KEYWDS PROTEIN, SUGAR BINDING PROTEIN, ANTIVIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.L.MCFEETERS,R.A.BYRD REVDAT 3 24-JUN-20 2JMV 1 COMPND SOURCE REMARK DBREF REVDAT 2 24-FEB-09 2JMV 1 VERSN REVDAT 1 12-JUN-07 2JMV 0 JRNL AUTH R.L.MCFEETERS,C.XIONG,B.R.O'KEEFE,H.R.BOKESCH,J.B.MCMAHON, JRNL AUTH 2 D.M.RATNER,R.CASTELLI,P.H.SEEBERGER,R.A.BYRD JRNL TITL THE NOVEL FOLD OF SCYTOVIRIN REVEALS A NEW TWIST FOR JRNL TITL 2 ANTIVIRAL ENTRY INHIBITORS JRNL REF J.MOL.BIOL. V. 369 451 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17434526 JRNL DOI 10.1016/J.JMB.2007.03.030 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.10, X-PLOR NIH 2.10, X-PLOR NIH 2.14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JMV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000100031. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 SCYTOVIRIN, 25 MM MES, 100 UM REMARK 210 EDTA, 10 UM SODIUM AZIDE, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D H(CCO)NH; REMARK 210 3D C(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 JMOD RDCS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH 2.14 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 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 ALA A 95 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 O GLY A 51 H THR A 53 1.06 REMARK 500 H CYS A 80 H PHE A 85 1.08 REMARK 500 O LYS A 44 H ASP A 46 1.18 REMARK 500 H CYS A 38 H GLN A 39 1.30 REMARK 500 O THR A 53 H HIS A 92 1.32 REMARK 500 H2 GLY A 1 OD1 ASP A 27 1.37 REMARK 500 H THR A 31 O GLN A 39 1.48 REMARK 500 O CYS A 32 H SER A 35 1.52 REMARK 500 O THR A 79 H SER A 81 1.53 REMARK 500 O THR A 31 H GLN A 39 1.58 REMARK 500 O ASP A 46 H GLY A 48 1.59 REMARK 500 O LYS A 44 N ASP A 46 1.91 REMARK 500 O GLY A 51 N THR A 53 2.02 REMARK 500 O PRO A 17 N ARG A 19 2.03 REMARK 500 OG1 THR A 53 O GLY A 76 2.04 REMARK 500 OG1 THR A 31 O GLN A 39 2.06 REMARK 500 O THR A 31 O GLN A 39 2.06 REMARK 500 O THR A 79 N SER A 81 2.09 REMARK 500 O GLY A 51 O THR A 53 2.11 REMARK 500 O THR A 79 N SER A 82 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 GLY A 1 N GLY A 1 CA -0.166 REMARK 500 1 PRO A 4 CA PRO A 4 C -0.168 REMARK 500 1 THR A 5 C TYR A 6 N 0.152 REMARK 500 1 TYR A 6 CB TYR A 6 CG 0.246 REMARK 500 1 TYR A 6 CA TYR A 6 C -0.271 REMARK 500 1 CYS A 7 N CYS A 7 CA -0.163 REMARK 500 1 ALA A 11 N ALA A 11 CA -0.131 REMARK 500 1 GLY A 15 C GLY A 16 N -0.156 REMARK 500 1 ARG A 19 CA ARG A 19 C -0.226 REMARK 500 1 ARG A 19 C CYS A 20 N 0.223 REMARK 500 1 CYS A 20 CB CYS A 20 SG 0.136 REMARK 500 1 CYS A 26 CB CYS A 26 SG 0.126 REMARK 500 1 GLY A 28 CA GLY A 28 C 0.119 REMARK 500 1 ARG A 30 CA ARG A 30 CB 0.203 REMARK 500 1 THR A 31 C THR A 31 O -0.150 REMARK 500 1 CYS A 32 N CYS A 32 CA 0.132 REMARK 500 1 SER A 33 CA SER A 33 CB -0.101 REMARK 500 1 SER A 34 C SER A 35 N 0.159 REMARK 500 1 PHE A 37 N PHE A 37 CA -0.140 REMARK 500 1 PHE A 37 C CYS A 38 N 0.177 REMARK 500 1 SER A 42 CA SER A 42 CB 0.116 REMARK 500 1 LYS A 44 CA LYS A 44 C -0.166 REMARK 500 1 GLY A 51 N GLY A 51 CA -0.154 REMARK 500 1 GLY A 51 CA GLY A 51 C -0.097 REMARK 500 1 GLY A 51 C GLY A 51 O -0.136 REMARK 500 1 THR A 53 CB THR A 53 OG1 -0.127 REMARK 500 1 TYR A 54 C CYS A 55 N 0.140 REMARK 500 1 ALA A 59 CA ALA A 59 CB -0.128 REMARK 500 1 LYS A 72 C GLN A 73 N -0.206 REMARK 500 1 GLN A 73 CA GLN A 73 CB 0.153 REMARK 500 1 CYS A 74 CB CYS A 74 SG 0.134 REMARK 500 1 ASP A 75 N ASP A 75 CA 0.140 REMARK 500 1 ASP A 75 CG ASP A 75 OD1 -0.152 REMARK 500 1 CYS A 80 CB CYS A 80 SG 0.212 REMARK 500 1 CYS A 80 C SER A 81 N -0.140 REMARK 500 1 SER A 82 CA SER A 82 CB -0.094 REMARK 500 1 GLY A 84 CA GLY A 84 C -0.113 REMARK 500 1 PHE A 85 N PHE A 85 CA -0.149 REMARK 500 1 CYS A 86 N CYS A 86 CA 0.141 REMARK 500 1 CYS A 86 CA CYS A 86 CB -0.115 REMARK 500 1 CYS A 86 CB CYS A 86 SG 0.182 REMARK 500 1 GLY A 91 N GLY A 91 CA 0.151 REMARK 500 1 GLY A 91 CA GLY A 91 C 0.246 REMARK 500 1 HIS A 92 N HIS A 92 CA 0.155 REMARK 500 2 GLY A 1 N GLY A 1 CA -0.161 REMARK 500 2 PRO A 4 CA PRO A 4 C -0.163 REMARK 500 2 THR A 5 C TYR A 6 N 0.160 REMARK 500 2 TYR A 6 CB TYR A 6 CG 0.244 REMARK 500 2 TYR A 6 CA TYR A 6 C -0.289 REMARK 500 2 CYS A 7 N CYS A 7 CA -0.180 REMARK 500 REMARK 500 THIS ENTRY HAS 860 BOND DEVIATIONS. 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 2 CYS A 26 CB - CA - C ANGL. DEV. = 8.1 DEGREES REMARK 500 3 CYS A 26 CB - CA - C ANGL. DEV. = 7.7 DEGREES REMARK 500 4 CYS A 26 CB - CA - C ANGL. DEV. = 8.1 DEGREES REMARK 500 7 CYS A 80 N - CA - CB ANGL. DEV. = 10.1 DEGREES REMARK 500 11 CYS A 80 N - CA - CB ANGL. DEV. = 9.5 DEGREES REMARK 500 13 CYS A 26 CB - CA - C ANGL. DEV. = 7.6 DEGREES REMARK 500 15 CYS A 80 N - CA - CB ANGL. DEV. = 10.2 DEGREES REMARK 500 16 ARG A 30 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 17 CYS A 26 CB - CA - C ANGL. DEV. = 7.2 DEGREES REMARK 500 18 CYS A 80 N - CA - CB ANGL. DEV. = 10.1 DEGREES REMARK 500 19 CYS A 80 N - CA - CB ANGL. DEV. = 9.3 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 SER A 2 -68.77 -97.41 REMARK 500 1 PRO A 4 85.56 -57.72 REMARK 500 1 THR A 5 -27.28 152.30 REMARK 500 1 TYR A 6 -26.35 -36.54 REMARK 500 1 TRP A 8 107.47 -38.29 REMARK 500 1 ASN A 9 -38.81 -28.58 REMARK 500 1 ALA A 11 114.28 -162.61 REMARK 500 1 ASN A 12 38.52 157.14 REMARK 500 1 ASN A 13 161.90 175.44 REMARK 500 1 PRO A 17 -144.03 -70.04 REMARK 500 1 ASN A 18 -8.94 -38.67 REMARK 500 1 ARG A 19 92.57 86.24 REMARK 500 1 CYS A 20 118.45 -9.10 REMARK 500 1 GLN A 25 -9.76 95.99 REMARK 500 1 ALA A 29 -30.73 140.09 REMARK 500 1 ARG A 30 169.16 -44.02 REMARK 500 1 CYS A 32 -168.75 -79.97 REMARK 500 1 SER A 35 -7.98 67.24 REMARK 500 1 PHE A 37 80.21 174.63 REMARK 500 1 CYS A 38 19.24 -171.26 REMARK 500 1 ARG A 43 67.79 26.72 REMARK 500 1 LYS A 44 101.49 -40.18 REMARK 500 1 PRO A 45 65.74 -51.60 REMARK 500 1 PRO A 47 55.95 -66.87 REMARK 500 1 PRO A 49 -84.05 -58.05 REMARK 500 1 PRO A 52 27.21 -39.68 REMARK 500 1 TYR A 54 130.28 163.50 REMARK 500 1 CYS A 55 -37.44 -130.17 REMARK 500 1 TRP A 56 -122.30 -109.90 REMARK 500 1 ASP A 57 10.74 156.61 REMARK 500 1 GLU A 58 76.80 175.49 REMARK 500 1 ASN A 61 153.25 -44.25 REMARK 500 1 PRO A 65 -177.77 -59.60 REMARK 500 1 ASN A 66 -20.00 -43.59 REMARK 500 1 ARG A 67 123.09 75.88 REMARK 500 1 CYS A 68 -92.56 -159.04 REMARK 500 1 SER A 69 -35.58 87.70 REMARK 500 1 SER A 71 35.72 161.86 REMARK 500 1 LYS A 72 29.18 -143.98 REMARK 500 1 GLN A 73 45.79 163.95 REMARK 500 1 CYS A 74 -146.79 -111.27 REMARK 500 1 ASP A 75 -97.31 -106.45 REMARK 500 1 CYS A 80 38.52 -3.78 REMARK 500 1 SER A 81 -14.73 91.09 REMARK 500 1 SER A 82 10.18 159.14 REMARK 500 1 PHE A 85 -82.67 -146.49 REMARK 500 1 GLN A 87 -42.13 163.53 REMARK 500 1 THR A 89 -63.30 -129.55 REMARK 500 1 ALA A 90 122.95 91.05 REMARK 500 1 HIS A 92 126.47 59.70 REMARK 500 REMARK 500 THIS ENTRY HAS 1040 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS REMARK 999 NOT AVAILABLE AT THE UNP SEQUENCE DATABASE. DBREF 2JMV A 1 95 UNP P86041 SVN_SCYVA 1 95 SEQRES 1 A 95 GLY SER GLY PRO THR TYR CYS TRP ASN GLU ALA ASN ASN SEQRES 2 A 95 PRO GLY GLY PRO ASN ARG CYS SER ASN ASN LYS GLN CYS SEQRES 3 A 95 ASP GLY ALA ARG THR CYS SER SER SER GLY PHE CYS GLN SEQRES 4 A 95 GLY THR SER ARG LYS PRO ASP PRO GLY PRO LYS GLY PRO SEQRES 5 A 95 THR TYR CYS TRP ASP GLU ALA LYS ASN PRO GLY GLY PRO SEQRES 6 A 95 ASN ARG CYS SER ASN SER LYS GLN CYS ASP GLY ALA ARG SEQRES 7 A 95 THR CYS SER SER SER GLY PHE CYS GLN GLY THR ALA GLY SEQRES 8 A 95 HIS ALA ALA ALA SSBOND 1 CYS A 7 CYS A 55 1555 1555 2.17 SSBOND 2 CYS A 20 CYS A 26 1555 1555 2.09 SSBOND 3 CYS A 32 CYS A 38 1555 1555 1.95 SSBOND 4 CYS A 68 CYS A 74 1555 1555 1.99 SSBOND 5 CYS A 74 CYS A 80 1555 1555 2.97 SSBOND 6 CYS A 80 CYS A 86 1555 1555 2.25 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 283 0 0 0 0 0 0 6 0 0 0 8 END