HEADER FLUORESCENT PROTEIN 21-FEB-24 8YDO TITLE CRYSTAL STRUCTURE OF DKEIMA570 CAVEAT 8YDO GYC B 63 HAS WRONG CHIRALITY AT ATOM CA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE STOKES SHIFT FLUORESCENT PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONTIPORA SP. 20; SOURCE 3 ORGANISM_TAXID: 321802; SOURCE 4 GENE: DKEIMA570; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LARGE STOKE SHIFT FLUORESCENT PROTEIN, DKEIMA570, TKEIMA, FLUORESCENT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.H.NAM REVDAT 1 03-APR-24 8YDO 0 JRNL AUTH K.H.NAM JRNL TITL CRYSTAL STRUCTURE OF DKEIMA570 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 51704 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2741 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3773 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 235 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6956 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 527 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.91000 REMARK 3 B12 (A**2) : -0.14000 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): 0.193 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.715 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7148 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6516 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9676 ; 1.640 ; 1.662 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15116 ; 1.455 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 860 ; 7.847 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 356 ;34.172 ;22.697 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1192 ;15.213 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.891 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 888 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8060 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1612 ; 0.001 ; 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): 3472 ; 2.597 ; 2.935 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3470 ; 2.579 ; 2.933 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4324 ; 3.419 ; 4.380 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4324 ; 3.405 ; 4.379 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3676 ; 4.107 ; 3.343 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3677 ; 4.106 ; 3.344 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5353 ; 5.955 ; 4.839 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7748 ; 6.993 ;34.516 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7654 ; 6.993 ;34.264 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK 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 8YDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54496 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.37500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA-CACODYLATE, MAGNESIUM ACETATE, REMARK 280 POLYETHYLENE GLYCOL 8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,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 34.43800 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 68.87600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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. (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 MET A 1 REMARK 465 VAL A 2 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 MET C 1 REMARK 465 VAL C 2 REMARK 465 MET D 1 REMARK 465 VAL D 2 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 O HOH A 417 O HOH A 432 2.05 REMARK 500 O HOH A 313 O HOH A 382 2.10 REMARK 500 O HOH A 416 O HOH B 359 2.14 REMARK 500 OE1 GLU A 86 NZ LYS A 182 2.15 REMARK 500 N SER A 3 O HOH A 301 2.17 REMARK 500 O HOH C 448 O HOH C 451 2.17 REMARK 500 O HOH A 312 O HOH A 402 2.18 REMARK 500 O HOH C 428 O HOH C 437 2.18 REMARK 500 OE1 GLU C 86 NZ LYS C 182 2.18 REMARK 500 O HOH C 375 O HOH C 391 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 399 O HOH D 407 1565 2.05 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 MET C 9 CG MET C 9 SD -0.157 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 MET A 9 CG - SD - CE ANGL. DEV. = -10.7 DEGREES REMARK 500 ASN B 129 CB - CA - C ANGL. DEV. = -13.6 DEGREES REMARK 500 MET C 9 CA - CB - CG ANGL. DEV. = -10.9 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 ASN A 125 21.47 82.18 REMARK 500 HIS B 201 147.12 -170.45 REMARK 500 SER C 200 138.85 -171.63 REMARK 500 PHE D 69 57.80 -92.87 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 GLY B 166 GLY B 167 149.86 REMARK 500 GLY D 166 GLY D 167 147.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YDO A 1 222 UNP Q1JU63 Q1JU63_9CNID 1 222 DBREF 8YDO B 1 222 UNP Q1JU63 Q1JU63_9CNID 1 222 DBREF 8YDO C 1 222 UNP Q1JU63 Q1JU63_9CNID 1 222 DBREF 8YDO D 1 222 UNP Q1JU63 Q1JU63_9CNID 1 222 SEQADV 8YDO GYC A 63 UNP Q1JU63 CYS 63 CHROMOPHORE SEQADV 8YDO GYC A 63 UNP Q1JU63 TYR 64 CHROMOPHORE SEQADV 8YDO GYC A 63 UNP Q1JU63 GLY 65 CHROMOPHORE SEQADV 8YDO VAL A 192 UNP Q1JU63 ILE 192 CONFLICT SEQADV 8YDO GYC B 63 UNP Q1JU63 CYS 63 CHROMOPHORE SEQADV 8YDO GYC B 63 UNP Q1JU63 TYR 64 CHROMOPHORE SEQADV 8YDO GYC B 63 UNP Q1JU63 GLY 65 CHROMOPHORE SEQADV 8YDO VAL B 192 UNP Q1JU63 ILE 192 CONFLICT SEQADV 8YDO GYC C 63 UNP Q1JU63 CYS 63 CHROMOPHORE SEQADV 8YDO GYC C 63 UNP Q1JU63 TYR 64 CHROMOPHORE SEQADV 8YDO GYC C 63 UNP Q1JU63 GLY 65 CHROMOPHORE SEQADV 8YDO VAL C 192 UNP Q1JU63 ILE 192 CONFLICT SEQADV 8YDO GYC D 63 UNP Q1JU63 CYS 63 CHROMOPHORE SEQADV 8YDO GYC D 63 UNP Q1JU63 TYR 64 CHROMOPHORE SEQADV 8YDO GYC D 63 UNP Q1JU63 GLY 65 CHROMOPHORE SEQADV 8YDO VAL D 192 UNP Q1JU63 ILE 192 CONFLICT SEQRES 1 A 220 MET VAL SER VAL ILE ALA LYS GLN MET THR TYR LYS VAL SEQRES 2 A 220 TYR MET SER GLY THR VAL ASN GLY HIS TYR PHE GLU VAL SEQRES 3 A 220 GLU GLY ASP GLY LYS GLY LYS PRO TYR GLU GLY GLU GLN SEQRES 4 A 220 THR VAL LYS LEU THR VAL THR LYS GLY GLY PRO LEU PRO SEQRES 5 A 220 PHE ALA TRP ASP ILE LEU SER PRO LEU MET GYC SER ILE SEQRES 6 A 220 PRO PHE THR LYS TYR PRO GLU ASP ILE PRO ASP TYR VAL SEQRES 7 A 220 LYS GLN SER PHE PRO GLU GLY TYR THR TRP GLU ARG THR SEQRES 8 A 220 MET ASN PHE GLU ASP GLY ALA VAL CYS THR VAL SER ASN SEQRES 9 A 220 ASP SER SER ILE GLN GLY ASN CYS PHE ILE TYR ASN VAL SEQRES 10 A 220 LYS ILE SER GLY THR ASN PHE PRO PRO ASN GLY PRO VAL SEQRES 11 A 220 MET GLN LYS LYS THR GLN GLY TRP GLU PRO SER THR GLU SEQRES 12 A 220 ARG LEU PHE ALA ARG ASP GLY MET LEU ILE GLY ASN ASP SEQRES 13 A 220 TYR MET ALA LEU LYS LEU GLU GLY GLY GLY HIS TYR LEU SEQRES 14 A 220 CYS GLU PHE LYS SER THR TYR LYS ALA LYS LYS PRO VAL SEQRES 15 A 220 ARG MET PRO GLY TYR HIS TYR VAL ASP ARG LYS LEU ASP SEQRES 16 A 220 VAL THR SER HIS ASN ARG ASP TYR THR SER VAL GLU GLN SEQRES 17 A 220 CYS GLU ILE ALA ILE ALA ARG HIS SER LEU LEU GLY SEQRES 1 B 220 MET VAL SER VAL ILE ALA LYS GLN MET THR TYR LYS VAL SEQRES 2 B 220 TYR MET SER GLY THR VAL ASN GLY HIS TYR PHE GLU VAL SEQRES 3 B 220 GLU GLY ASP GLY LYS GLY LYS PRO TYR GLU GLY GLU GLN SEQRES 4 B 220 THR VAL LYS LEU THR VAL THR LYS GLY GLY PRO LEU PRO SEQRES 5 B 220 PHE ALA TRP ASP ILE LEU SER PRO LEU MET GYC SER ILE SEQRES 6 B 220 PRO PHE THR LYS TYR PRO GLU ASP ILE PRO ASP TYR VAL SEQRES 7 B 220 LYS GLN SER PHE PRO GLU GLY TYR THR TRP GLU ARG THR SEQRES 8 B 220 MET ASN PHE GLU ASP GLY ALA VAL CYS THR VAL SER ASN SEQRES 9 B 220 ASP SER SER ILE GLN GLY ASN CYS PHE ILE TYR ASN VAL SEQRES 10 B 220 LYS ILE SER GLY THR ASN PHE PRO PRO ASN GLY PRO VAL SEQRES 11 B 220 MET GLN LYS LYS THR GLN GLY TRP GLU PRO SER THR GLU SEQRES 12 B 220 ARG LEU PHE ALA ARG ASP GLY MET LEU ILE GLY ASN ASP SEQRES 13 B 220 TYR MET ALA LEU LYS LEU GLU GLY GLY GLY HIS TYR LEU SEQRES 14 B 220 CYS GLU PHE LYS SER THR TYR LYS ALA LYS LYS PRO VAL SEQRES 15 B 220 ARG MET PRO GLY TYR HIS TYR VAL ASP ARG LYS LEU ASP SEQRES 16 B 220 VAL THR SER HIS ASN ARG ASP TYR THR SER VAL GLU GLN SEQRES 17 B 220 CYS GLU ILE ALA ILE ALA ARG HIS SER LEU LEU GLY SEQRES 1 C 220 MET VAL SER VAL ILE ALA LYS GLN MET THR TYR LYS VAL SEQRES 2 C 220 TYR MET SER GLY THR VAL ASN GLY HIS TYR PHE GLU VAL SEQRES 3 C 220 GLU GLY ASP GLY LYS GLY LYS PRO TYR GLU GLY GLU GLN SEQRES 4 C 220 THR VAL LYS LEU THR VAL THR LYS GLY GLY PRO LEU PRO SEQRES 5 C 220 PHE ALA TRP ASP ILE LEU SER PRO LEU MET GYC SER ILE SEQRES 6 C 220 PRO PHE THR LYS TYR PRO GLU ASP ILE PRO ASP TYR VAL SEQRES 7 C 220 LYS GLN SER PHE PRO GLU GLY TYR THR TRP GLU ARG THR SEQRES 8 C 220 MET ASN PHE GLU ASP GLY ALA VAL CYS THR VAL SER ASN SEQRES 9 C 220 ASP SER SER ILE GLN GLY ASN CYS PHE ILE TYR ASN VAL SEQRES 10 C 220 LYS ILE SER GLY THR ASN PHE PRO PRO ASN GLY PRO VAL SEQRES 11 C 220 MET GLN LYS LYS THR GLN GLY TRP GLU PRO SER THR GLU SEQRES 12 C 220 ARG LEU PHE ALA ARG ASP GLY MET LEU ILE GLY ASN ASP SEQRES 13 C 220 TYR MET ALA LEU LYS LEU GLU GLY GLY GLY HIS TYR LEU SEQRES 14 C 220 CYS GLU PHE LYS SER THR TYR LYS ALA LYS LYS PRO VAL SEQRES 15 C 220 ARG MET PRO GLY TYR HIS TYR VAL ASP ARG LYS LEU ASP SEQRES 16 C 220 VAL THR SER HIS ASN ARG ASP TYR THR SER VAL GLU GLN SEQRES 17 C 220 CYS GLU ILE ALA ILE ALA ARG HIS SER LEU LEU GLY SEQRES 1 D 220 MET VAL SER VAL ILE ALA LYS GLN MET THR TYR LYS VAL SEQRES 2 D 220 TYR MET SER GLY THR VAL ASN GLY HIS TYR PHE GLU VAL SEQRES 3 D 220 GLU GLY ASP GLY LYS GLY LYS PRO TYR GLU GLY GLU GLN SEQRES 4 D 220 THR VAL LYS LEU THR VAL THR LYS GLY GLY PRO LEU PRO SEQRES 5 D 220 PHE ALA TRP ASP ILE LEU SER PRO LEU MET GYC SER ILE SEQRES 6 D 220 PRO PHE THR LYS TYR PRO GLU ASP ILE PRO ASP TYR VAL SEQRES 7 D 220 LYS GLN SER PHE PRO GLU GLY TYR THR TRP GLU ARG THR SEQRES 8 D 220 MET ASN PHE GLU ASP GLY ALA VAL CYS THR VAL SER ASN SEQRES 9 D 220 ASP SER SER ILE GLN GLY ASN CYS PHE ILE TYR ASN VAL SEQRES 10 D 220 LYS ILE SER GLY THR ASN PHE PRO PRO ASN GLY PRO VAL SEQRES 11 D 220 MET GLN LYS LYS THR GLN GLY TRP GLU PRO SER THR GLU SEQRES 12 D 220 ARG LEU PHE ALA ARG ASP GLY MET LEU ILE GLY ASN ASP SEQRES 13 D 220 TYR MET ALA LEU LYS LEU GLU GLY GLY GLY HIS TYR LEU SEQRES 14 D 220 CYS GLU PHE LYS SER THR TYR LYS ALA LYS LYS PRO VAL SEQRES 15 D 220 ARG MET PRO GLY TYR HIS TYR VAL ASP ARG LYS LEU ASP SEQRES 16 D 220 VAL THR SER HIS ASN ARG ASP TYR THR SER VAL GLU GLN SEQRES 17 D 220 CYS GLU ILE ALA ILE ALA ARG HIS SER LEU LEU GLY MODRES 8YDO GYC A 63 CYS CHROMOPHORE MODRES 8YDO GYC A 63 TYR CHROMOPHORE MODRES 8YDO GYC A 63 GLY CHROMOPHORE MODRES 8YDO GYC B 63 CYS CHROMOPHORE MODRES 8YDO GYC B 63 TYR CHROMOPHORE MODRES 8YDO GYC B 63 GLY CHROMOPHORE MODRES 8YDO GYC C 63 CYS CHROMOPHORE MODRES 8YDO GYC C 63 TYR CHROMOPHORE MODRES 8YDO GYC C 63 GLY CHROMOPHORE MODRES 8YDO GYC D 63 CYS CHROMOPHORE MODRES 8YDO GYC D 63 TYR CHROMOPHORE MODRES 8YDO GYC D 63 GLY CHROMOPHORE HET GYC A 63 21 HET GYC B 63 21 HET GYC C 63 21 HET GYC D 63 21 HETNAM GYC [(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4- HETNAM 2 GYC HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 GYC YL]ACETIC ACID HETSYN GYC CHROMOPHORE (CYS-TYR-GLY) FORMUL 1 GYC 4(C14 H15 N3 O4 S) FORMUL 5 HOH *527(H2 O) HELIX 1 AA1 PRO A 34 GLU A 36 5 3 HELIX 2 AA2 ALA A 54 MET A 62 5 9 HELIX 3 AA3 ASP A 78 SER A 83 1 6 HELIX 4 AA4 PRO B 34 GLU B 36 5 3 HELIX 5 AA5 ALA B 54 MET B 62 5 9 HELIX 6 AA6 ASP B 78 SER B 83 1 6 HELIX 7 AA7 ALA C 54 MET C 62 5 9 HELIX 8 AA8 ASP C 78 SER C 83 1 6 HELIX 9 AA9 ALA D 54 MET D 62 5 9 HELIX 10 AB1 ASP D 78 SER D 83 1 6 SHEET 1 AA113 THR A 137 TRP A 140 0 SHEET 2 AA113 MET A 153 LEU A 164 -1 O LYS A 163 N GLY A 139 SHEET 3 AA113 HIS A 169 ALA A 180 -1 O SER A 176 N GLY A 156 SHEET 4 AA113 TYR A 88 PHE A 96 -1 N THR A 89 O LYS A 179 SHEET 5 AA113 VAL A 101 GLN A 111 -1 O SER A 108 N TYR A 88 SHEET 6 AA113 CYS A 114 THR A 124 -1 O THR A 124 N VAL A 101 SHEET 7 AA113 MET A 9 VAL A 19 1 N LYS A 12 O TYR A 117 SHEET 8 AA113 HIS A 22 LYS A 33 -1 O VAL A 26 N MET A 15 SHEET 9 AA113 GLU A 38 LYS A 47 -1 O THR A 44 N GLU A 27 SHEET 10 AA113 SER A 207 ARG A 217 -1 O VAL A 208 N LEU A 43 SHEET 11 AA113 HIS A 190 HIS A 201 -1 N TYR A 191 O ARG A 217 SHEET 12 AA113 SER A 143 ARG A 150 -1 N LEU A 147 O HIS A 190 SHEET 13 AA113 MET A 153 LEU A 164 -1 O ASN A 157 N ARG A 146 SHEET 1 AA213 THR B 137 TRP B 140 0 SHEET 2 AA213 MET B 153 LEU B 164 -1 O LYS B 163 N GLN B 138 SHEET 3 AA213 HIS B 169 ALA B 180 -1 O TYR B 170 N LEU B 162 SHEET 4 AA213 TYR B 88 PHE B 96 -1 N THR B 89 O LYS B 179 SHEET 5 AA213 VAL B 101 GLN B 111 -1 O SER B 108 N TYR B 88 SHEET 6 AA213 CYS B 114 THR B 124 -1 O ILE B 116 N SER B 109 SHEET 7 AA213 MET B 9 VAL B 19 1 N LYS B 12 O TYR B 117 SHEET 8 AA213 HIS B 22 LYS B 33 -1 O VAL B 26 N MET B 15 SHEET 9 AA213 GLU B 38 LYS B 47 -1 O LYS B 42 N ASP B 29 SHEET 10 AA213 SER B 207 ARG B 217 -1 O VAL B 208 N LEU B 43 SHEET 11 AA213 HIS B 190 HIS B 201 -1 N ASP B 193 O ILE B 215 SHEET 12 AA213 SER B 143 ARG B 150 -1 N LEU B 147 O HIS B 190 SHEET 13 AA213 MET B 153 LEU B 164 -1 O ILE B 155 N PHE B 148 SHEET 1 AA313 THR C 137 TRP C 140 0 SHEET 2 AA313 MET C 153 LEU C 164 -1 O LYS C 163 N GLN C 138 SHEET 3 AA313 HIS C 169 ALA C 180 -1 O TYR C 170 N LEU C 162 SHEET 4 AA313 TYR C 88 PHE C 96 -1 N THR C 89 O LYS C 179 SHEET 5 AA313 VAL C 101 GLN C 111 -1 O SER C 108 N TYR C 88 SHEET 6 AA313 CYS C 114 THR C 124 -1 O ASN C 118 N ASP C 107 SHEET 7 AA313 MET C 9 VAL C 19 1 N THR C 18 O GLY C 123 SHEET 8 AA313 HIS C 22 LYS C 33 -1 O VAL C 26 N MET C 15 SHEET 9 AA313 GLU C 38 LYS C 47 -1 O THR C 44 N GLU C 27 SHEET 10 AA313 SER C 207 ARG C 217 -1 O VAL C 208 N LEU C 43 SHEET 11 AA313 HIS C 190 HIS C 201 -1 N SER C 200 O GLU C 209 SHEET 12 AA313 SER C 143 ARG C 150 -1 N LEU C 147 O HIS C 190 SHEET 13 AA313 MET C 153 LEU C 164 -1 O ASN C 157 N ARG C 146 SHEET 1 AA413 THR D 137 TRP D 140 0 SHEET 2 AA413 MET D 153 LEU D 164 -1 O LYS D 163 N GLN D 138 SHEET 3 AA413 HIS D 169 ALA D 180 -1 O TYR D 170 N LEU D 162 SHEET 4 AA413 TYR D 88 PHE D 96 -1 N THR D 89 O LYS D 179 SHEET 5 AA413 VAL D 101 GLN D 111 -1 O ASN D 106 N TRP D 90 SHEET 6 AA413 CYS D 114 THR D 124 -1 O LYS D 120 N SER D 105 SHEET 7 AA413 MET D 9 VAL D 19 1 N THR D 18 O GLY D 123 SHEET 8 AA413 HIS D 22 LYS D 33 -1 O VAL D 26 N MET D 15 SHEET 9 AA413 GLU D 38 LYS D 47 -1 O THR D 40 N LYS D 31 SHEET 10 AA413 SER D 207 ARG D 217 -1 O VAL D 208 N LEU D 43 SHEET 11 AA413 HIS D 190 HIS D 201 -1 N ASP D 193 O ILE D 215 SHEET 12 AA413 SER D 143 ARG D 150 -1 N SER D 143 O ARG D 194 SHEET 13 AA413 MET D 153 LEU D 164 -1 O ILE D 155 N PHE D 148 LINK C MET A 62 N1 GYC A 63 1555 1555 1.39 LINK C3 GYC A 63 N SER A 66 1555 1555 1.37 LINK C MET B 62 N1 GYC B 63 1555 1555 1.43 LINK C3 GYC B 63 N SER B 66 1555 1555 1.37 LINK C MET C 62 N1 GYC C 63 1555 1555 1.52 LINK C3 GYC C 63 N SER C 66 1555 1555 1.37 LINK C MET D 62 N1 GYC D 63 1555 1555 1.48 LINK C3 GYC D 63 N SER D 66 1555 1555 1.37 CISPEP 1 GLY A 49 PRO A 50 0 -7.42 CISPEP 2 PHE A 84 PRO A 85 0 7.16 CISPEP 3 GLY B 49 PRO B 50 0 -7.06 CISPEP 4 PHE B 84 PRO B 85 0 5.00 CISPEP 5 GLY C 49 PRO C 50 0 -4.35 CISPEP 6 PHE C 84 PRO C 85 0 8.00 CISPEP 7 GLY D 49 PRO D 50 0 -4.69 CISPEP 8 PHE D 84 PRO D 85 0 4.45 CRYST1 83.713 83.713 103.314 90.00 90.00 120.00 P 31 12 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 0.011946 0.006897 0.000000 0.00000 SCALE2 0.000000 0.013794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009679 0.00000