10 20 30 40 50 60 70 80 1L5E - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIVIRAL PROTEIN 06-MAR-02 1L5E
TITLE THE DOMAIN-SWAPPED DIMER OF CV-N IN SOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYANOVIRIN-N; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CV-N; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC ELLIPSOSPORUM; SOURCE 3 ORGANISM_TAXID: 45916; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS 3D DOMAIN-SWAPPING, CYANOVIRIN-N, PROTEIN FOLDING, NMR, X- KEYWDS 2 RAY, ANTIVIRAL PROTEIN
EXPDTA SOLUTION NMR
AUTHOR L.G.BARRIENTOS,J.M.LOUIS,I.BOTOS,T.MORI,Z.HAN,B.R.O'KEEFE, AUTHOR 2 M.R.BOYD,A.WLODAWER,A.M.GRONENBORN
REVDAT 3 24-FEB-09 1L5E 1 VERSN REVDAT 2 01-APR-03 1L5E 1 JRNL REVDAT 1 05-JUN-02 1L5E 0
JRNL AUTH L.G.BARRIENTOS,J.M.LOUIS,I.BOTOS,T.MORI,Z.HAN, JRNL AUTH 2 B.R.O'KEEFE,M.R.BOYD,A.WLODAWER,A.M.GRONENBORN JRNL TITL THE DOMAIN-SWAPPED DIMER OF CYANOVIRIN-N IS IN A JRNL TITL 2 METASTABLE FOLDED STATE: RECONCILIATION OF X-RAY JRNL TITL 3 AND NMR STRUCTURES. JRNL REF STRUCTURE V. 10 673 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12015150 JRNL DOI 10.1016/S0969-2126(02)00758-X
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PALES REMARK 3 AUTHORS : M.ZWECKSTETTER, A.BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE COORDINATES OF THE INDIVIDUAL REMARK 3 DOMAINS OF THE DOMAIN SWAPPED DIMER CV-N WERE TAKEN DIRECTLY REMARK 3 FROM THE X-RAY COORDINATES, 3EZM AND 1L5B. THE ONLY PROTONS REMARK 3 ADDED ARE THE HNE1 OF W(49/150) AND ALL THE BACKBONE AMIDE REMARK 3 PROTONS (HN), SINCE DOMAIN-DOMAIN ORIENTATION WAS BASED ONLY REMARK 3 ON HN/HNE1 RESIDUAL DIPOLAR COUPLINGS. THE STARTING REMARK 3 COORDINATES WERE THOSE OF TWO PSEUDO-MONOMER UNITS (AB' AND A' REMARK 3 B) EXTRACTED FROM THE REFINED TRIGONAL 1.5 X-RAY STRUCTURE, IN REMARK 3 WHICH PROLINE 51 AT THE JUNCTION BETWEEN A AND B WAS REMOVED, REMARK 3 ALLOWING FOR FREE ROTATION AROUND THIS JUNCTION. WE THEN REMARK 3 TREATED AB' AND A'B AS TWO INDEPENDENT SUB-DOMAINS. ASSUMING REMARK 3 THAT THE ORIENTATION OF THE TWO SUB-DOMAINS IS FIXED IN REMARK 3 SOLUTION (AT LEAST TO A FIRST APPROXIMATION), THE PRINCIPAL REMARK 3 AXIS SYSTEMS, OR ALIGNMENT FRAMES, OF SUB-DOMAINS AB' AND A'B REMARK 3 SHOULD BE EQUIVALENT TO THE ALIGNMENT SYSTEM OF THE ENTIRE REMARK 3 MOLECULE AND, VICE VERSA, TO EACH OTHER. USING THE RESIDUAL REMARK 3 DIPOLAR COUPLINGS WE CALCULATED THE ORDER TENSOR PRINCIPAL REMARK 3 AXIS SYSTEMS FOR EACH DOMAIN. ROTATION OF PSEUDO SUB-DOMAIN A' REMARK 3 B AROUND THE HINGE AT AMINO ACID POSITION 51 UNTIL A REMARK 3 SUPERPOSITION OF THE INDIVIDUAL COORDINATE FRAMES WAS OBTAINED REMARK 3 YIELDED THE FINAL MODEL OF THE SOLUTION DIMER.
REMARK 4 REMARK 4 1L5E COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-02. REMARK 100 THE RCSB ID CODE IS RCSB015656.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.150 MM PROTEIN IN 25 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 8.0 AND 0.02 % NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D IPAP [15N-1H]-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, PALES REMARK 210 METHOD USED : DETERMINATION OF THE DOMAIN REMARK 210 ORIENTATION FOR THE SOLUTION REMARK 210 STRUCTURE OF THE DIMER WAS REMARK 210 CARRIED OUT USING A PROCEDURE REMARK 210 ANALOGOUS TO THE ONE DESCRIBED REMARK 210 FOR DETERMINING THE RELATIVE REMARK 210 DOMAIN ORIENTATION IN A TWO- REMARK 210 DOMAIN PROTEIN FRAGMENT OF A REMARK 210 LECTIN. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: RESIDUAL DIPOLAR COUPLINGS WERE MEASURED IN THE REMARK 210 PRESENCE OF A COLLOIDAL PHAGE SOLUTION OF 11.5 MG/ML PF1.
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 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 VAL A 39 CB - CA - C ANGL. DEV. = -11.7 DEGREES REMARK 500 GLN A 50 N - CA - CB ANGL. DEV. = -15.8 DEGREES REMARK 500 VAL B 140 CB - CA - C ANGL. DEV. = -11.9 DEGREES REMARK 500 GLN B 151 N - CA - CB ANGL. DEV. = -15.8 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 GLN A 50 -155.93 -124.94 REMARK 500 ASN A 53 -174.73 169.59 REMARK 500 SER A 67 5.10 -151.08 REMARK 500 GLN B 151 -155.28 -124.60 REMARK 500 ASN B 154 -174.65 169.40 REMARK 500 SER B 168 5.10 -151.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL A 39 14.44 REMARK 500 VAL B 140 14.57 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EZM RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF CYANOVIRIN-N, RESTRAINED REMARK 900 REGULARIZED MEAN COORDINATES REMARK 900 RELATED ID: 3EZM RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF CYANOVIRIN-N; DOMAIN-SWAPPED DIMER REMARK 900 RELATED ID: 1L5B RELATED DB: PDB REMARK 900 DOMAIN-SWAPPED CYANOVIRIN-N DIMER
DBREF 1L5E A 1 101 UNP P81180 CVN_NOSEL 1 101 DBREF 1L5E B 102 202 UNP P81180 CVN_NOSEL 1 101
SEQRES 1 A 101 LEU GLY LYS PHE SER GLN THR CYS TYR ASN SER ALA ILE SEQRES 2 A 101 GLN GLY SER VAL LEU THR SER THR CYS GLU ARG THR ASN SEQRES 3 A 101 GLY GLY TYR ASN THR SER SER ILE ASP LEU ASN SER VAL SEQRES 4 A 101 ILE GLU ASN VAL ASP GLY SER LEU LYS TRP GLN PRO SER SEQRES 5 A 101 ASN PHE ILE GLU THR CYS ARG ASN THR GLN LEU ALA GLY SEQRES 6 A 101 SER SER GLU LEU ALA ALA GLU CYS LYS THR ARG ALA GLN SEQRES 7 A 101 GLN PHE VAL SER THR LYS ILE ASN LEU ASP ASP HIS ILE SEQRES 8 A 101 ALA ASN ILE ASP GLY THR LEU LYS TYR GLU SEQRES 1 B 101 LEU GLY LYS PHE SER GLN THR CYS TYR ASN SER ALA ILE SEQRES 2 B 101 GLN GLY SER VAL LEU THR SER THR CYS GLU ARG THR ASN SEQRES 3 B 101 GLY GLY TYR ASN THR SER SER ILE ASP LEU ASN SER VAL SEQRES 4 B 101 ILE GLU ASN VAL ASP GLY SER LEU LYS TRP GLN PRO SER SEQRES 5 B 101 ASN PHE ILE GLU THR CYS ARG ASN THR GLN LEU ALA GLY SEQRES 6 B 101 SER SER GLU LEU ALA ALA GLU CYS LYS THR ARG ALA GLN SEQRES 7 B 101 GLN PHE VAL SER THR LYS ILE ASN LEU ASP ASP HIS ILE SEQRES 8 B 101 ALA ASN ILE ASP GLY THR LEU LYS TYR GLU
HELIX 1 1 LYS A 3 GLN A 6 5 4 HELIX 2 2 LYS B 104 GLN B 107 5 4
SHEET 1 A 3 CYS A 8 GLN A 14 0 SHEET 2 A 3 VAL A 17 GLU A 23 -1 O THR A 19 N ALA A 12 SHEET 3 A 3 TYR A 29 ASP A 35 -1 O ASN A 30 N CYS A 22 SHEET 1 B 2 ILE A 40 VAL A 43 0 SHEET 2 B 2 SER A 46 TRP A 49 -1 O LYS A 48 N GLU A 41 SHEET 1 C 3 CYS A 58 ALA A 64 0 SHEET 2 C 3 GLU A 68 LYS A 74 -1 O GLU A 68 N ALA A 64 SHEET 3 C 3 PHE A 80 ASN A 86 -1 O ILE A 85 N LEU A 69 SHEET 1 D 2 ILE A 91 ILE A 94 0 SHEET 2 D 2 THR A 97 TYR A 100 -1 O LYS A 99 N ALA A 92 SHEET 1 E 3 CYS B 109 GLN B 115 0 SHEET 2 E 3 VAL B 118 GLU B 124 -1 O THR B 120 N ALA B 113 SHEET 3 E 3 TYR B 130 ASP B 136 -1 O ASN B 131 N CYS B 123 SHEET 1 F 2 ILE B 141 VAL B 144 0 SHEET 2 F 2 SER B 147 TRP B 150 -1 O LYS B 149 N GLU B 142 SHEET 1 G 3 CYS B 159 ALA B 165 0 SHEET 2 G 3 GLU B 169 LYS B 175 -1 O GLU B 169 N ALA B 165 SHEET 3 G 3 PHE B 181 ASN B 187 -1 O ILE B 186 N LEU B 170 SHEET 1 H 2 ILE B 192 ILE B 195 0 SHEET 2 H 2 THR B 198 TYR B 201 -1 O LYS B 200 N ALA B 193
SSBOND 1 CYS A 8 CYS A 22 1555 1555 2.03 SSBOND 2 CYS A 58 CYS A 73 1555 1555 2.04 SSBOND 3 CYS B 109 CYS B 123 1555 1555 2.03 SSBOND 4 CYS B 159 CYS B 174 1555 1555 2.04
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