HEADER PLANT PROTEIN 06-APR-17 5VF5 TITLE CRYSTAL STRUCTURE OF THE VICILIN FROM SOLANUM MELONGENA, RE-REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SM80.1 VICILIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM MELONGENA; SOURCE 3 ORGANISM_COMMON: EGGPLANT; SOURCE 4 ORGANISM_TAXID: 4111; SOURCE 5 TISSUE: SEED KEYWDS 7S VICILIN SM80.1 PLANT PROTEIN SEQUENCE ASSIGNMENT RE-REFINEMENT, KEYWDS 2 PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.J.POREBSKI,A.WLODAWER,Z.DAUTER,W.MINOR,R.STANFIELD,M.JASKOLSKI, AUTHOR 2 E.POZHARSKI,C.X.WEICHENBERGER,B.RUPP REVDAT 5 04-OCT-23 5VF5 1 REMARK REVDAT 4 13-APR-22 5VF5 1 AUTHOR JRNL LINK REVDAT 3 01-JAN-20 5VF5 1 REMARK REVDAT 2 14-FEB-18 5VF5 1 JRNL REVDAT 1 06-DEC-17 5VF5 0 JRNL AUTH A.WLODAWER,Z.DAUTER,P.J.POREBSKI,W.MINOR,R.STANFIELD, JRNL AUTH 2 M.JASKOLSKI,E.POZHARSKI,C.X.WEICHENBERGER,B.RUPP JRNL TITL DETECT, CORRECT, RETRACT: HOW TO MANAGE INCORRECT STRUCTURAL JRNL TITL 2 MODELS. JRNL REF FEBS J. V. 285 444 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 29113027 JRNL DOI 10.1111/FEBS.14320 REMARK 0 REMARK 0 THIS ENTRY 5VF5 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 5CAD, DETERMINED BY A.JAIN,A.KUMAR,D.M.SALUNKE REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 5CAD REMARK 0 AUTH A.JAIN,A.KUMAR,D.M.SALUNKE REMARK 0 TITL CRYSTAL STRUCTURE OF THE VICILIN FROM SOLANUM MELONGENA REMARK 0 TITL 2 REVEALS EXISTENCE OF DIFFERENT ANIONIC LIGANDS IN REMARK 0 TITL 3 STRUCTURALLY SIMILAR POCKETS. REMARK 0 REF SCI REP V. 6 23600 2016 REMARK 0 REFN ESSN 2045-2322 REMARK 0 PMID 27004988 REMARK 0 DOI 10.1038/SREP23600 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 66897 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 + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3556 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4888 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 270 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2948 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 1.77000 REMARK 3 B12 (A**2) : -0.27000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.969 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3371 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3088 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4585 ; 1.686 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7176 ; 1.520 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 6.402 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;36.380 ;23.125 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 591 ;12.830 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;17.566 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 478 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3896 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 787 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1597 ; 2.133 ; 1.745 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1595 ; 2.120 ;35.079 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2010 ; 2.451 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2011 ; 2.450 ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1774 ; 3.536 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1772 ; 3.538 ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2543 ; 4.038 ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3638 ; 4.223 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3639 ; 4.222 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3336 ; 5.063 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3235 ;11.256 ; 2.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5VF5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 22.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.06100 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) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5CAD REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 5CAD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-CL, 1.5 M SODIUM MALONATE, REMARK 280 10% PEG 3350, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 59.66500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.44760 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.73000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 59.66500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 34.44760 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 52.73000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 59.66500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 34.44760 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.73000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 59.66500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 34.44760 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.73000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 59.66500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 34.44760 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.73000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 59.66500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 34.44760 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.73000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 68.89521 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 105.46000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 68.89521 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 105.46000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 68.89521 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 105.46000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 68.89521 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 105.46000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 68.89521 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 105.46000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 68.89521 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 105.46000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 59.66500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 103.34281 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -59.66500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 103.34281 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 666 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 915 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 1 REMARK 465 GLY A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 ARG A 198 REMARK 465 SER A 199 REMARK 465 THR A 200 REMARK 465 GLN A 201 REMARK 465 GLN A 202 REMARK 465 THR A 203 REMARK 465 ARG A 204 REMARK 465 GLY A 205 REMARK 465 ARG A 286 REMARK 465 GLN A 287 REMARK 465 GLY A 288 REMARK 465 ARG A 289 REMARK 465 GLY A 290 REMARK 465 GLN A 291 REMARK 465 GLY A 292 REMARK 465 GLY A 293 REMARK 465 GLU A 294 REMARK 465 GLN A 295 REMARK 465 GLU A 296 REMARK 465 GLN A 297 REMARK 465 GLU A 298 REMARK 465 GLN A 299 REMARK 465 GLU A 300 REMARK 465 GLU A 301 REMARK 465 ARG A 399 REMARK 465 GLN A 400 REMARK 465 GLN A 401 REMARK 465 GLN A 402 REMARK 465 PRO A 403 REMARK 465 GLY A 404 REMARK 465 GLU A 405 REMARK 465 ARG A 406 REMARK 465 GLY A 407 REMARK 465 GLU A 408 REMARK 465 GLU A 409 REMARK 465 GLY A 410 REMARK 465 ARG A 411 REMARK 465 LYS A 412 REMARK 465 GLY A 413 REMARK 465 GLN A 414 REMARK 465 ASP A 415 REMARK 465 GLN A 416 REMARK 465 TYR A 417 REMARK 465 LEU A 418 REMARK 465 SER A 419 REMARK 465 SER A 420 REMARK 465 ILE A 421 REMARK 465 LEU A 422 REMARK 465 ASP A 423 REMARK 465 PHE A 424 REMARK 465 VAL A 425 REMARK 465 PHE A 426 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 5 CG CD OE1 NE2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 GLN A 17 CD OE1 NE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 GLN A 208 CG CD OE1 NE2 REMARK 470 GLU A 236 CD OE1 OE2 REMARK 470 GLU A 397 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASN A 352 O HOH A 601 2.16 REMARK 500 O HIS A 195 O HOH A 602 2.17 REMARK 500 OG SER A 231 OE1 GLU A 233 2.18 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 GLY A 333 N - CA - C ANGL. DEV. = 19.4 DEGREES REMARK 500 ARG A 350 NE - CZ - NH1 ANGL. DEV. = -3.3 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 ASP A 68 30.17 -97.58 REMARK 500 ASN A 117 -33.62 -135.38 REMARK 500 ASN A 130 -128.91 -98.15 REMARK 500 GLU A 303 153.49 -49.04 REMARK 500 TYR A 391 -59.25 76.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 951 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 952 DISTANCE = 6.00 ANGSTROMS 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 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 25 O REMARK 620 2 GLY A 28 O 85.8 REMARK 620 3 HOH A 827 O 82.0 101.3 REMARK 620 4 HOH A 827 O 92.6 173.0 85.2 REMARK 620 5 HOH A 847 O 91.4 86.4 169.4 86.9 REMARK 620 6 HOH A 910 O 167.6 96.4 85.5 86.7 101.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 503 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 281 SG REMARK 620 2 HIS A 283 ND1 120.5 REMARK 620 3 HIS A 325 NE2 122.5 116.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CAD RELATED DB: PDB REMARK 900 THIS ENTRY 5VF5 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 900 DATA IN 5CAD DBREF 5VF5 A 1 426 PDB 5VF5 5VF5 1 426 SEQRES 1 A 426 PRO GLY ARG GLU GLN GLN GLU GLU ASN VAL PRO TYR LEU SEQRES 2 A 426 PHE LYS SER GLN ARG PHE GLN SER ARG PHE ARG ALA SER SEQRES 3 A 426 HIS GLY ASP PHE ARG ILE LEU PRO LYS PHE THR GLN ARG SEQRES 4 A 426 SER GLN LEU LEU ARG GLY ILE GLU LYS PHE ARG VAL SER SEQRES 5 A 426 VAL ILE GLU LEU GLU PRO GLN SER PHE MET LEU PRO HIS SEQRES 6 A 426 HIS CSD ASP GLY GLU ALA ILE PHE VAL VAL VAL ARG GLY SEQRES 7 A 426 GLN GLY THR ILE SER ILE ALA GLU GLN ASP GLU LYS ASN SEQRES 8 A 426 SER PHE ASN LEU GLU ARG GLY ASP VAL LEU ARG LEU HIS SEQRES 9 A 426 GLY GLY SER THR ILE HIS LEU LEU ASN ARG ASP ASN ASN SEQRES 10 A 426 GLU LYS PHE PHE VAL TYR VAL LEU ALA LYS SER VAL ASN SEQRES 11 A 426 ALA PRO GLY GLN VAL GLN GLU TYR PHE SER ALA GLY GLY SEQRES 12 A 426 GLU ASN PRO GLU SER PHE TYR ARG ALA PHE SER SER ASP SEQRES 13 A 426 ILE LEU GLU SER ALA PHE ASN THR GLN ARG ASP ARG ILE SEQRES 14 A 426 GLU ARG LEU PHE ARG GLN GLN LYS GLN GLY ALA ILE ILE SEQRES 15 A 426 LYS ALA SER GLU GLU GLN ILE ARG ALA ILE SER GLU HIS SEQRES 16 A 426 ALA SER ARG SER THR GLN GLN THR ARG GLY ARG THR GLN SEQRES 17 A 426 GLY PRO PHE ASN LEU MET LYS GLU ARG PRO GLN PHE GLY SEQRES 18 A 426 SER ARG PHE GLY GLN PHE ILE GLU ALA SER PRO GLU ARG SEQRES 19 A 426 PHE GLU GLN LEU ARG ASP LEU ASP ALA ALA VAL ALA PHE SEQRES 20 A 426 MET ASN ILE ASN GLN GLY GLY MET VAL LEU PRO TYR TYR SEQRES 21 A 426 ASN SER ARG SER THR ARG VAL VAL MET VAL VAL GLU GLY SEQRES 22 A 426 ASN ALA ARG PHE GLU MET ALA CYS PRO HIS LEU GLY ARG SEQRES 23 A 426 GLN GLY ARG GLY GLN GLY GLY GLU GLN GLU GLN GLU GLN SEQRES 24 A 426 GLU GLU GLY GLU VAL HIS TYR GLN LYS VAL ARG GLY ASN SEQRES 25 A 426 LEU ASN VAL GLY ASP VAL LEU VAL ILE PRO ALA GLY HIS SEQRES 26 A 426 PRO ILE THR PHE ILE ALA THR GLY GLY SER ASN PHE ARG SEQRES 27 A 426 VAL VAL GLY PHE GLY ILE ASN ALA MET PHE ASN ARG LYS SEQRES 28 A 426 ASN PHE LEU ALA GLY ARG GLU ASN ILE TRP ARG ASN ILE SEQRES 29 A 426 ASP ARG GLU ALA LYS GLU LEU SER PHE ASN MET PRO GLY SEQRES 30 A 426 ARG GLU VAL GLU GLU ILE PHE GLN LYS GLN ASP GLN SER SEQRES 31 A 426 TYR PHE VAL ALA GLY PRO GLU HIS ARG GLN GLN GLN PRO SEQRES 32 A 426 GLY GLU ARG GLY GLU GLU GLY ARG LYS GLY GLN ASP GLN SEQRES 33 A 426 TYR LEU SER SER ILE LEU ASP PHE VAL PHE HET CSD A 67 11 HET NA A 501 1 HET ACT A 502 4 HET CU A 503 1 HET PEG A 504 7 HET MLI A 505 7 HETNAM CSD 3-SULFINOALANINE HETNAM NA SODIUM ION HETNAM ACT ACETATE ION HETNAM CU COPPER (II) ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MLI MALONATE ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 NA NA 1+ FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 CU CU 2+ FORMUL 5 PEG C4 H10 O3 FORMUL 6 MLI C3 H2 O4 2- FORMUL 7 HOH *352(H2 O) HELIX 1 AA1 GLN A 5 VAL A 10 5 6 HELIX 2 AA2 LYS A 15 PHE A 19 5 5 HELIX 3 AA3 LYS A 35 ARG A 39 5 5 HELIX 4 AA4 SER A 40 GLU A 47 5 8 HELIX 5 AA5 SER A 148 PHE A 153 5 6 HELIX 6 AA6 SER A 154 ASN A 163 1 10 HELIX 7 AA7 GLN A 165 PHE A 173 1 9 HELIX 8 AA8 SER A 185 SER A 193 1 9 HELIX 9 AA9 PHE A 235 ARG A 239 5 5 HELIX 10 AB1 ASN A 359 ILE A 364 5 6 HELIX 11 AB2 ASP A 365 ASN A 374 1 10 HELIX 12 AB3 PRO A 376 LYS A 386 1 11 SHEET 1 AA1 7 LEU A 13 PHE A 14 0 SHEET 2 AA1 7 VAL A 318 ILE A 321 -1 O VAL A 318 N PHE A 14 SHEET 3 AA1 7 THR A 265 GLU A 272 -1 N VAL A 268 O LEU A 319 SHEET 4 AA1 7 PHE A 337 ILE A 344 -1 O VAL A 340 N MET A 269 SHEET 5 AA1 7 ALA A 243 ILE A 250 -1 N ALA A 246 O GLY A 341 SHEET 6 AA1 7 GLY A 225 ALA A 230 -1 N ILE A 228 O PHE A 247 SHEET 7 AA1 7 PHE A 220 SER A 222 -1 N PHE A 220 O PHE A 227 SHEET 1 AA2 6 GLN A 20 SER A 21 0 SHEET 2 AA2 6 GLY A 28 ILE A 32 -1 O ILE A 32 N GLN A 20 SHEET 3 AA2 6 PHE A 49 LEU A 56 -1 O GLU A 55 N ASP A 29 SHEET 4 AA2 6 PHE A 120 SER A 128 -1 O ALA A 126 N ARG A 50 SHEET 5 AA2 6 GLY A 69 ARG A 77 -1 N VAL A 74 O TYR A 123 SHEET 6 AA2 6 VAL A 100 LEU A 103 -1 O LEU A 101 N PHE A 73 SHEET 1 AA3 5 LYS A 90 GLU A 96 0 SHEET 2 AA3 5 GLN A 79 ALA A 85 -1 N ILE A 84 O ASN A 91 SHEET 3 AA3 5 THR A 108 ASN A 113 -1 O THR A 108 N ALA A 85 SHEET 4 AA3 5 SER A 60 CSD A 67 -1 N HIS A 65 O ILE A 109 SHEET 5 AA3 5 GLU A 137 PHE A 139 -1 O TYR A 138 N HIS A 66 SHEET 1 AA4 5 LYS A 90 GLU A 96 0 SHEET 2 AA4 5 GLN A 79 ALA A 85 -1 N ILE A 84 O ASN A 91 SHEET 3 AA4 5 THR A 108 ASN A 113 -1 O THR A 108 N ALA A 85 SHEET 4 AA4 5 SER A 60 CSD A 67 -1 N HIS A 65 O ILE A 109 SHEET 5 AA4 5 ILE A 181 LYS A 183 -1 O ILE A 182 N PHE A 61 SHEET 1 AA5 5 GLN A 307 LEU A 313 0 SHEET 2 AA5 5 ALA A 275 CYS A 281 -1 N CYS A 281 O GLN A 307 SHEET 3 AA5 5 ILE A 327 ALA A 331 -1 O ILE A 330 N ARG A 276 SHEET 4 AA5 5 GLY A 254 ASN A 261 -1 N TYR A 259 O ILE A 327 SHEET 5 AA5 5 LYS A 351 PHE A 353 -1 O ASN A 352 N TYR A 260 SHEET 1 AA6 5 GLN A 307 LEU A 313 0 SHEET 2 AA6 5 ALA A 275 CYS A 281 -1 N CYS A 281 O GLN A 307 SHEET 3 AA6 5 ILE A 327 ALA A 331 -1 O ILE A 330 N ARG A 276 SHEET 4 AA6 5 GLY A 254 ASN A 261 -1 N TYR A 259 O ILE A 327 SHEET 5 AA6 5 PHE A 392 ALA A 394 -1 O VAL A 393 N MET A 255 LINK C HIS A 66 N CSD A 67 1555 1555 1.32 LINK C CSD A 67 N ASP A 68 1555 1555 1.33 LINK O ALA A 25 NA NA A 501 1555 1555 2.35 LINK O GLY A 28 NA NA A 501 1555 1555 2.36 LINK SG CYS A 281 CU A CU A 503 1555 1555 2.25 LINK ND1AHIS A 283 CU A CU A 503 1555 1555 1.94 LINK NE2 HIS A 325 CU A CU A 503 1555 1555 2.00 LINK NA NA A 501 O HOH A 827 1555 1555 2.46 LINK NA NA A 501 O HOH A 827 1555 4556 2.44 LINK NA NA A 501 O HOH A 847 1555 1555 2.43 LINK NA NA A 501 O HOH A 910 1555 1555 2.34 CISPEP 1 ASN A 145 PRO A 146 0 -6.75 SITE 1 AC1 5 ALA A 25 GLY A 28 HOH A 827 HOH A 847 SITE 2 AC1 5 HOH A 910 SITE 1 AC2 5 PHE A 227 TYR A 259 ASN A 261 ARG A 266 SITE 2 AC2 5 LYS A 351 SITE 1 AC3 5 TYR A 12 CYS A 281 PRO A 282 HIS A 283 SITE 2 AC3 5 HIS A 325 SITE 1 AC4 3 PHE A 224 GLY A 253 GLY A 395 SITE 1 AC5 11 LYS A 90 ASN A 91 SER A 92 HIS A 195 SITE 2 AC5 11 ASP A 365 ARG A 366 GLU A 367 HOH A 602 SITE 3 AC5 11 HOH A 661 HOH A 720 HOH A 838 CRYST1 119.330 119.330 158.190 90.00 90.00 120.00 H 3 2 18 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 0.008380 0.004838 0.000000 0.00000 SCALE2 0.000000 0.009677 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006322 0.00000