HEADER ANTIVIRAL PROTEIN 30-APR-08 3CZZ TITLE CRYSTAL STRUCTURE OF CYANOVIRIN-N DOMAIN B MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYANOVIRIN-N; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CV-N; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC ELLIPSOSPORUM; SOURCE 3 ORGANISM_TAXID: 45916; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS CYANOVIRIN-N, SUGAR BINDING PROTEIN, HIV-INACTIVATING, GP120, KEYWDS 2 ANTIVIRAL PROTEIN, PROTEIN SYNTHESIS INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR E.MATEI,W.FUREY,A.M.GRONENBORN REVDAT 4 01-NOV-23 3CZZ 1 REMARK REVDAT 3 10-NOV-21 3CZZ 1 SEQADV REVDAT 2 24-FEB-09 3CZZ 1 VERSN REVDAT 1 19-AUG-08 3CZZ 0 JRNL AUTH E.MATEI,W.FUREY,A.M.GRONENBORN JRNL TITL SOLUTION AND CRYSTAL STRUCTURES OF A SUGAR BINDING SITE JRNL TITL 2 MUTANT OF CYANOVIRIN-N: NO EVIDENCE OF DOMAIN SWAPPING. JRNL REF STRUCTURE V. 16 1183 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18682220 JRNL DOI 10.1016/J.STR.2008.05.011 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 995851.910 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 36955 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 3688 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.45 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4918 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 564 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 448 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.13 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.12 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.520 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.500 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.600 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.68 REMARK 3 BSOL : 250.0 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CZZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : HF VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37884 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 29.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.430 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.94 REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.1 REMARK 200 STARTING MODEL: 1L5B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 24% POLYETHYLE REMARK 280 MONOMETYL ETHER, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 17.08000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.89500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.89500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.08000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.01000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 HIS B 90 -3.75 -141.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L5B RELATED DB: PDB REMARK 900 DOMAIN-SWAPPED CYANOVIRIN-N DIMER REMARK 900 RELATED ID: 2Z21 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MONOVALENT MUTANT OF CYANOVIRIN-N REMARK 900 RELATED ID: 2EZM RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF THE MONOMER CV-N DBREF 3CZZ A 1 101 UNP P81180 CVN_NOSEL 1 101 DBREF 3CZZ B 1 101 UNP P81180 CVN_NOSEL 1 101 SEQADV 3CZZ ALA A 41 UNP P81180 GLU 41 ENGINEERED MUTATION SEQADV 3CZZ ALA A 42 UNP P81180 ASN 42 ENGINEERED MUTATION SEQADV 3CZZ GLY A 51 UNP P81180 PRO 51 ENGINEERED MUTATION SEQADV 3CZZ ALA A 57 UNP P81180 THR 57 ENGINEERED MUTATION SEQADV 3CZZ ALA A 76 UNP P81180 ARG 76 ENGINEERED MUTATION SEQADV 3CZZ GLY A 78 UNP P81180 GLN 78 ENGINEERED MUTATION SEQADV 3CZZ ALA B 41 UNP P81180 GLU 41 ENGINEERED MUTATION SEQADV 3CZZ ALA B 42 UNP P81180 ASN 42 ENGINEERED MUTATION SEQADV 3CZZ GLY B 51 UNP P81180 PRO 51 ENGINEERED MUTATION SEQADV 3CZZ ALA B 57 UNP P81180 THR 57 ENGINEERED MUTATION SEQADV 3CZZ ALA B 76 UNP P81180 ARG 76 ENGINEERED MUTATION SEQADV 3CZZ GLY B 78 UNP P81180 GLN 78 ENGINEERED MUTATION 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 ALA ALA VAL ASP GLY SER LEU LYS TRP GLN GLY SER SEQRES 5 A 101 ASN PHE ILE GLU ALA CYS ARG ASN THR GLN LEU ALA GLY SEQRES 6 A 101 SER SER GLU LEU ALA ALA GLU CYS LYS THR ALA ALA GLY 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 ALA ALA VAL ASP GLY SER LEU LYS TRP GLN GLY SER SEQRES 5 B 101 ASN PHE ILE GLU ALA CYS ARG ASN THR GLN LEU ALA GLY SEQRES 6 B 101 SER SER GLU LEU ALA ALA GLU CYS LYS THR ALA ALA GLY 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 FORMUL 3 HOH *448(H2 O) HELIX 1 1 LYS A 3 GLN A 6 5 4 HELIX 2 2 ASN A 37 VAL A 39 5 3 HELIX 3 3 ASN A 53 GLU A 56 5 4 HELIX 4 4 LYS B 3 GLN B 6 5 4 HELIX 5 5 ASN B 37 VAL B 39 5 3 HELIX 6 6 ASN B 53 GLU B 56 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 ALA A 41 VAL A 43 0 SHEET 2 B 2 SER A 46 LYS A 48 -1 O LYS A 48 N ALA 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 8 GLN B 14 0 SHEET 2 E 3 VAL B 17 GLU B 23 -1 O THR B 19 N ALA B 12 SHEET 3 E 3 TYR B 29 ASP B 35 -1 O ASN B 30 N CYS B 22 SHEET 1 F 2 ALA B 41 VAL B 43 0 SHEET 2 F 2 SER B 46 LYS B 48 -1 O LYS B 48 N ALA B 41 SHEET 1 G 3 CYS B 58 ALA B 64 0 SHEET 2 G 3 GLU B 68 LYS B 74 -1 O GLU B 68 N ALA B 64 SHEET 3 G 3 PHE B 80 ASN B 86 -1 O VAL B 81 N CYS B 73 SHEET 1 H 2 ILE B 91 ILE B 94 0 SHEET 2 H 2 THR B 97 TYR B 100 -1 O LYS B 99 N ALA B 92 SSBOND 1 CYS A 8 CYS A 22 1555 1555 2.04 SSBOND 2 CYS A 58 CYS A 73 1555 1555 2.03 SSBOND 3 CYS B 8 CYS B 22 1555 1555 2.04 SSBOND 4 CYS B 58 CYS B 73 1555 1555 2.03 CRYST1 34.160 58.020 87.790 90.00 90.00 90.00 P 21 21 21 8 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 0.029274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011391 0.00000