HEADER LUMINESCENT PROTEIN 27-FEB-12 4DXO TITLE CRYSTAL STRUCTURE OF A RECONSTRUCTED KAEDE-TYPE RED FLUORESCENT TITLE 2 PROTEIN, LEA X(6) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEA X(6) GFP-LIKE PROTEINS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KAEDE-TYPE RED FLUORESCENT PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: ARTIFICIAL; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEM-T KEYWDS BETA BARREL, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KIM,R.FROMME,R.M.WACHTER REVDAT 5 20-NOV-24 4DXO 1 REMARK REVDAT 4 15-NOV-23 4DXO 1 LINK ATOM REVDAT 3 22-APR-15 4DXO 1 JRNL REVDAT 2 04-FEB-15 4DXO 1 REMARK REVDAT 1 27-FEB-13 4DXO 0 JRNL AUTH H.KIM,T.ZOU,C.MODI,K.DORNER,T.J.GRUNKEMEYER,L.CHEN,R.FROMME, JRNL AUTH 2 M.V.MATZ,S.B.OZKAN,R.M.WACHTER JRNL TITL A HINGE MIGRATION MECHANISM UNLOCKS THE EVOLUTION OF JRNL TITL 2 GREEN-TO-RED PHOTOCONVERSION IN GFP-LIKE PROTEINS. JRNL REF STRUCTURE V. 23 34 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25565105 JRNL DOI 10.1016/J.STR.2014.11.011 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 7527 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 382 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 534 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.4590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1726 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : -0.07000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.314 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.681 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1736 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1226 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2330 ; 2.070 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2957 ; 1.065 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 205 ; 7.861 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;36.708 ;24.051 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 299 ;19.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;10.244 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 237 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1900 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 363 ; 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): 1037 ; 1.501 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 431 ; 0.437 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1659 ; 2.553 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 699 ; 3.508 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 671 ; 5.356 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2962 ; 2.010 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 78 ;11.076 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2923 ; 2.598 ; 3.000 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4DXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 39.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.07M TRIS, 0.2 M MAGNESIUM CHLORIDE, REMARK 280 16% PEG 4000, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 23.82500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.17000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.71500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.82500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.17000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.71500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.82500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.17000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.71500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.82500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.17000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.71500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 219 REMARK 465 PRO A 220 REMARK 465 ARG A 221 REMARK 465 GLN A 222 REMARK 465 ALA A 223 REMARK 465 LYS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 7 C REMARK 480 GLY A 16 C REMARK 480 LYS A 22 C REMARK 480 PHE A 52 C REMARK 480 GLU A 96 CD REMARK 480 ASP A 97 CG REMARK 480 ASN A 105 CG REMARK 480 GLY A 111 C REMARK 480 ASP A 121 CG REMARK 480 ASN A 128 CG REMARK 480 TYR A 147 CZ REMARK 480 ASP A 156 CG 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 ASP A 121 O HOH A 404 2.17 REMARK 500 N ILE A 4 O HOH A 401 2.18 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 NZ LYS A 202 O HOH A 457 1655 1.79 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 ASP A 7 C ASP A 7 O -0.157 REMARK 500 ASP A 7 C MET A 8 N 0.185 REMARK 500 HIS A 21 NE2 HIS A 21 CD2 -0.070 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 ASP A 7 CB - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 ASP A 7 O - C - N ANGL. DEV. = 12.2 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 PHE A 68 57.55 -93.36 REMARK 500 ASP A 77 99.52 -67.01 REMARK 500 ASP A 150 49.40 35.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DXI RELATED DB: PDB REMARK 900 RELATED ID: 4DXM RELATED DB: PDB REMARK 900 RELATED ID: 4DXN RELATED DB: PDB REMARK 900 RELATED ID: 4DXP RELATED DB: PDB REMARK 900 RELATED ID: 4DXQ RELATED DB: PDB DBREF 4DXO A 1 230 PDB 4DXO 4DXO 1 230 SEQRES 1 A 228 MET SER VAL ILE LYS SER ASP MET LYS ILE LYS LEU ARG SEQRES 2 A 228 MET GLU GLY THR VAL ASN GLY HIS LYS PHE VAL ILE GLU SEQRES 3 A 228 GLY GLU GLY GLU GLY LYS PRO TYR GLU GLY THR GLN THR SEQRES 4 A 228 MET ASN LEU LYS VAL LYS GLU GLY ALA PRO LEU PRO PHE SEQRES 5 A 228 ALA TYR ASP ILE LEU THR THR ALA PHE CR8 ASN ARG VAL SEQRES 6 A 228 PHE ALA LYS TYR PRO LYS ASP ILE PRO ASP TYR PHE LYS SEQRES 7 A 228 GLN SER PHE PRO GLU GLY TYR SER TRP GLU ARG SER MET SEQRES 8 A 228 THR PHE GLU ASP GLY GLY ILE CYS THR ALA ARG ASN ASP SEQRES 9 A 228 ILE THR LEU GLU GLY ASP CYS PHE PHE ASN GLU ILE ARG SEQRES 10 A 228 PHE ASP GLY VAL ASN PHE PRO PRO ASN GLY PRO VAL MET SEQRES 11 A 228 GLN LYS LYS THR LEU LYS TRP GLU PRO SER THR GLU LYS SEQRES 12 A 228 MET TYR VAL ARG ASP GLY VAL LEU MET GLY ASP VAL ASN SEQRES 13 A 228 MET ALA LEU LEU LEU GLU GLY GLY GLY HIS TYR ARG CYS SEQRES 14 A 228 ASP PHE LYS THR THR TYR LYS ALA LYS LYS GLY VAL GLN SEQRES 15 A 228 LEU PRO ASP TYR HIS PHE VAL ASP HIS CYS ILE GLU ILE SEQRES 16 A 228 LEU SER HIS ASP LYS ASP TYR ASN ASN VAL LYS LEU TYR SEQRES 17 A 228 GLU HIS ALA VAL ALA HIS SER GLY LEU PRO ARG GLN ALA SEQRES 18 A 228 LYS HIS HIS HIS HIS HIS HIS MODRES 4DXO CR8 A 63 HIS MODRES 4DXO CR8 A 63 TYR MODRES 4DXO CR8 A 63 GLY HET CR8 A 63 25 HET NA A 301 1 HETNAM CR8 2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1- HETNAM 2 CR8 (CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1- HETNAM 3 CR8 YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE HETNAM NA SODIUM ION HETSYN CR8 CHROMOPHORE (HIS-TYR-GLY) FORMUL 1 CR8 C17 H16 N5 O4 1- FORMUL 2 NA NA 1+ FORMUL 3 HOH *60(H2 O) HELIX 1 1 ALA A 53 LEU A 57 5 5 HELIX 2 2 ASP A 77 SER A 82 1 6 SHEET 1 A13 THR A 136 TRP A 139 0 SHEET 2 A13 VAL A 152 LEU A 163 -1 O LEU A 162 N LEU A 137 SHEET 3 A13 HIS A 168 ALA A 179 -1 O TYR A 177 N LEU A 153 SHEET 4 A13 TYR A 87 PHE A 95 -1 N SER A 88 O LYS A 178 SHEET 5 A13 ILE A 100 GLU A 110 -1 O ALA A 103 N ARG A 91 SHEET 6 A13 CYS A 113 VAL A 123 -1 O PHE A 115 N THR A 108 SHEET 7 A13 MET A 8 VAL A 18 1 N ARG A 13 O ILE A 118 SHEET 8 A13 HIS A 21 LYS A 32 -1 O GLY A 29 N ILE A 10 SHEET 9 A13 THR A 37 GLU A 46 -1 O THR A 39 N GLU A 30 SHEET 10 A13 ASN A 206 HIS A 216 -1 O VAL A 207 N LEU A 42 SHEET 11 A13 HIS A 189 HIS A 200 -1 N ASP A 192 O VAL A 214 SHEET 12 A13 SER A 142 ARG A 149 -1 N SER A 142 O HIS A 193 SHEET 13 A13 VAL A 152 LEU A 163 -1 O ASP A 156 N LYS A 145 LINK C PHE A 61 N1 CR8 A 63 1555 1555 1.32 LINK C3 CR8 A 63 N ASN A 65 1555 1555 1.33 CISPEP 1 ALA A 48 PRO A 49 0 -7.89 CISPEP 2 PHE A 83 PRO A 84 0 8.42 CRYST1 47.650 78.340 119.430 90.00 90.00 90.00 I 2 2 2 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 0.020986 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008373 0.00000