10 20 30 40 50 60 70 80 3EKH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER FLUORESCENT PROTEIN 19-SEP-08 3EKH
TITLE CALCIUM-SATURATED GCAMP2 T116V/K378W MUTANT MONOMER
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOSIN LIGHT CHAIN KINASE, GREEN FLUORESCENT PROTEIN, COMPND 3 CALMODULIN CHIMERA; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE, AEQUOREA VICTORIA, RATTUS SOURCE 3 NORVEGICUS; SOURCE 4 ORGANISM_COMMON: JELLYFISH, RAT; SOURCE 5 ORGANISM_TAXID: 32630, 6100, 10116; SOURCE 6 GENE: GFP, CALM1, CALM, CAM, CAM1, CAMI; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PRSETA
KEYWDS GECI, GCAMP2, CPEGFP, CALMODULIN, M13 PEPTIDE, SIGNALING PROTEIN, KEYWDS 2 FLUORESCENT PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.AKERBOOM,J.D.VELEZ RIVERA,L.L.LOOGER,E.R.SCHREITER
REVDAT 6 21-JUN-17 3EKH 1 SOURCE DBREF SEQADV MODRES REVDAT 5 31-OCT-12 3EKH 1 DBREF REVDAT 4 13-JUL-11 3EKH 1 VERSN REVDAT 3 10-MAR-09 3EKH 1 JRNL REVDAT 2 30-DEC-08 3EKH 1 JRNL REVDAT 1 16-DEC-08 3EKH 0
JRNL AUTH J.AKERBOOM,J.D.RIVERA,M.M.GUILBE,E.C.MALAVE,H.H.HERNANDEZ, JRNL AUTH 2 L.TIAN,S.A.HIRES,J.S.MARVIN,L.L.LOOGER,E.R.SCHREITER JRNL TITL CRYSTAL STRUCTURES OF THE GCAMP CALCIUM SENSOR REVEAL THE JRNL TITL 2 MECHANISM OF FLUORESCENCE SIGNAL CHANGE AND AID RATIONAL JRNL TITL 3 DESIGN JRNL REF J.BIOL.CHEM. V. 284 6455 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19098007 JRNL DOI 10.1074/JBC.M807657200
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.M RODRIGUEZ GUILBE,E.C.ALFARO MALAVE,J.AKERBOOM, REMARK 1 AUTH 2 J.S.MARVIN,L.L.LOOGER,E.R.SCHREITER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CHARACTERIZATION OF REMARK 1 TITL 2 THE GENETICALLY ENCODED FLUORESCENT CALCIUM INDICATOR REMARK 1 TITL 3 PROTEIN GCAMP2 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 64 629 2008 REMARK 1 REFN ESSN 1744-3091
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 23.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 47172 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2546 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) : 3418 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3152 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 277 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.42000 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): 0.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.704 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3255 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2213 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4397 ; 1.332 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5410 ; 0.864 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 403 ; 5.938 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;33.779 ;25.301 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 587 ;13.964 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;17.944 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3662 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 644 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 645 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2206 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1525 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1736 ; 0.102 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 215 ; 0.170 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.135 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 23 ; 0.240 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.142 ; 0.200 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): 2055 ; 1.036 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 819 ; 0.178 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3186 ; 1.557 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1379 ; 2.169 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1207 ; 3.265 ; 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): 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 3EKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049435.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-08 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 : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DIAMOND(1,1,1) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.60100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 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: PDB ENTRY 3EK8 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM FORMATE DIHYDRATE, 15% REMARK 280 W/V POLYETHYLENE GLYCOL 3,350, PH 8, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 48.66350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.82400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.82400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.33175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.82400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.82400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.99525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.82400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.82400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.33175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.82400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.82400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.99525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.66350 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ARG A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 GLY A 11 REMARK 465 MET A 12 REMARK 465 ALA A 13 REMARK 465 SER A 14 REMARK 465 MET A 15 REMARK 465 THR A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 GLN A 19 REMARK 465 GLN A 20 REMARK 465 MET A 21 REMARK 465 GLY A 22 REMARK 465 ARG A 23 REMARK 465 ASP A 24 REMARK 465 LEU A 25 REMARK 465 TYR A 26 REMARK 465 ASP A 27 REMARK 465 ASP A 28 REMARK 465 ASP A 29 REMARK 465 ASP A 30 REMARK 465 LYS A 31 REMARK 465 ASP A 32 REMARK 465 LEU A 33 REMARK 465 ALA A 34 REMARK 465 THR A 35 REMARK 465 MET A 36 REMARK 465 VAL A 37 REMARK 465 ASP A 38 REMARK 465 GLY A 145 REMARK 465 MET A 146 REMARK 465 ASP A 147 REMARK 465 GLU A 148 REMARK 465 LEU A 149 REMARK 465 TYR A 150 REMARK 465 LYS A 151 REMARK 465 GLY A 152 REMARK 465 GLY A 153 REMARK 465 THR A 154 REMARK 465 GLY A 155 REMARK 465 GLY A 156 REMARK 465 SER A 157 REMARK 465 MET A 158 REMARK 465 ALA A 450 REMARK 465 LYS A 451
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 OE1 GLU A 269 O HOH A 705 2.07 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 ARG A 231 NE - CZ - NH2 ANGL. DEV. = -3.4 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 LEU A 60 72.65 58.83 REMARK 500 TYR A 301 -61.46 -93.52 REMARK 500 ARG A 304 81.68 -64.44 REMARK 500 ASP A 432 95.40 -68.93 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 650 DISTANCE = 6.48 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 CA A 453 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 323 OD1 REMARK 620 2 ASP A 325 OD1 83.9 REMARK 620 3 ASP A 327 OD1 85.4 79.4 REMARK 620 4 THR A 329 O 85.1 158.9 81.8 REMARK 620 5 GLU A 334 OE1 98.4 72.9 151.5 126.7 REMARK 620 6 GLU A 334 OE2 111.4 124.1 151.2 76.8 52.3 REMARK 620 7 HOH A 536 O 162.9 80.3 85.4 107.7 83.2 83.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 454 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 359 OD2 REMARK 620 2 ASP A 361 OD1 78.1 REMARK 620 3 ASN A 363 OD1 88.1 73.0 REMARK 620 4 THR A 365 O 87.6 152.1 82.8 REMARK 620 5 ASP A 367 OD1 173.8 96.0 92.0 98.5 REMARK 620 6 GLU A 370 OE1 104.7 129.1 155.9 77.6 77.4 REMARK 620 7 GLU A 370 OE2 91.9 75.8 148.1 129.0 84.8 53.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 455 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 396 OD2 REMARK 620 2 ASP A 398 OD2 79.9 REMARK 620 3 ASN A 400 OD1 85.0 75.6 REMARK 620 4 TYR A 402 O 86.4 150.1 76.9 REMARK 620 5 GLU A 407 OE1 98.1 77.8 152.2 130.8 REMARK 620 6 GLU A 407 OE2 112.4 128.5 151.1 81.3 51.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 456 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 432 OD1 REMARK 620 2 ASP A 434 OD2 73.7 REMARK 620 3 ASP A 436 OD1 84.3 70.9 REMARK 620 4 GLN A 438 O 95.3 150.6 81.1 REMARK 620 5 GLU A 443 OE1 115.8 127.5 154.7 81.8 REMARK 620 6 GLU A 443 OE2 84.1 82.5 153.1 124.1 50.4 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 453 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 454 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 455 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 456
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EK4 RELATED DB: PDB REMARK 900 CALCIUM-SATURATED STATE OF GCAMP2 MONOMER REMARK 900 RELATED ID: 3EK7 RELATED DB: PDB REMARK 900 CALCIUM-SATURATED GCAMP2 DIMER REMARK 900 RELATED ID: 3EK8 RELATED DB: PDB REMARK 900 CALCIUM-SATURATED GCAMP2 T116V/G174R MONOMER REMARK 900 RELATED ID: 3EKJ RELATED DB: PDB
REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND REMARK 999 GLY67 CONSTITUTE THE CHROMOPHORE CRO. THE AUTHOR STATES THAT ANY REMARK 999 DIFFERENCES WITH DATABASE SEQUENCE LIKELY REPRESENT MUTATIONS REMARK 999 INTRODUCED DURING VARIOUS ENGINEERING STEPS.
DBREF 3EKH A 1 61 PDB 3EKH 3EKH 1 61 DBREF 3EKH A 62 151 UNP P42212 GFP_AEQVI 149 238 DBREF 3EKH A 160 302 UNP P42212 GFP_AEQVI 2 144 DBREF 3EKH A 305 451 UNP P0DP29 CALM1_RAT 3 149
SEQADV 3EKH MET A 1 PDB INITIATING METHIONINE SEQADV 3EKH ALA A 76 UNP P42212 VAL 163 SEE REMARK 999 SEQADV 3EKH GLY A 88 UNP P42212 SER 175 SEE REMARK 999 SEQADV 3EKH TYR A 93 UNP P42212 ASP 180 SEE REMARK 999 SEQADV 3EKH VAL A 116 UNP P42212 THR 203 ENGINEERED MUTATION SEQADV 3EKH LYS A 119 UNP P42212 ALA 206 SEE REMARK 999 SEQADV 3EKH LEU A 144 UNP P42212 HIS 231 SEE REMARK 999 SEQADV 3EKH GLY A 152 UNP P42212 LINKER SEQADV 3EKH GLY A 153 UNP P42212 LINKER SEQADV 3EKH THR A 154 UNP P42212 LINKER SEQADV 3EKH GLY A 155 UNP P42212 LINKER SEQADV 3EKH GLY A 156 UNP P42212 LINKER SEQADV 3EKH SER A 157 UNP P42212 LINKER SEQADV 3EKH MET A 158 UNP P42212 LINKER SEQADV 3EKH VAL A 159 UNP P42212 LINKER SEQADV 3EKH LEU A 222 UNP P42212 PHE 64 SEE REMARK 999 SEQADV 3EKH CRO A 224 UNP P42212 SER 65 CHROMOPHORE SEQADV 3EKH A UNP P42212 TYR 66 DELETION SEQADV 3EKH A UNP P42212 GLY 67 DELETION SEQADV 3EKH ILE A 251 UNP P42212 VAL 93 SEE REMARK 999 SEQADV 3EKH THR A 303 UNP P42212 LINKER SEQADV 3EKH ARG A 304 UNP P42212 LINKER SEQADV 3EKH TRP A 378 UNP P0DP29 LYS 76 ENGINEERED MUTATION
SEQRES 1 A 449 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 449 SER MET THR GLY GLY GLN GLN MET GLY ARG ASP LEU TYR SEQRES 3 A 449 ASP ASP ASP ASP LYS ASP LEU ALA THR MET VAL ASP SER SEQRES 4 A 449 SER ARG ARG LYS TRP ASN LYS THR GLY HIS ALA VAL ARG SEQRES 5 A 449 ALA ILE GLY ARG LEU SER SER LEU GLU ASN VAL TYR ILE SEQRES 6 A 449 MET ALA ASP LYS GLN LYS ASN GLY ILE LYS ALA ASN PHE SEQRES 7 A 449 LYS ILE ARG HIS ASN ILE GLU ASP GLY GLY VAL GLN LEU SEQRES 8 A 449 ALA TYR HIS TYR GLN GLN ASN THR PRO ILE GLY ASP GLY SEQRES 9 A 449 PRO VAL LEU LEU PRO ASP ASN HIS TYR LEU SER VAL GLN SEQRES 10 A 449 SER LYS LEU SER LYS ASP PRO ASN GLU LYS ARG ASP HIS SEQRES 11 A 449 MET VAL LEU LEU GLU PHE VAL THR ALA ALA GLY ILE THR SEQRES 12 A 449 LEU GLY MET ASP GLU LEU TYR LYS GLY GLY THR GLY GLY SEQRES 13 A 449 SER MET VAL SER LYS GLY GLU GLU LEU PHE THR GLY VAL SEQRES 14 A 449 VAL PRO ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY SEQRES 15 A 449 HIS LYS PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA SEQRES 16 A 449 THR TYR GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR SEQRES 17 A 449 GLY LYS LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR SEQRES 18 A 449 LEU CRO VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET SEQRES 19 A 449 LYS GLN HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY SEQRES 20 A 449 TYR ILE GLN GLU ARG THR ILE PHE PHE LYS ASP ASP GLY SEQRES 21 A 449 ASN TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP SEQRES 22 A 449 THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE SEQRES 23 A 449 LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR SEQRES 24 A 449 ASN THR ARG ASP GLN LEU THR GLU GLU GLN ILE ALA GLU SEQRES 25 A 449 PHE LYS GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP SEQRES 26 A 449 GLY THR ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SEQRES 27 A 449 SER LEU GLY GLN ASN PRO THR GLU ALA GLU LEU GLN ASP SEQRES 28 A 449 MET ILE ASN GLU VAL ASP ALA ASP GLY ASN GLY THR ILE SEQRES 29 A 449 ASP PHE PRO GLU PHE LEU THR MET MET ALA ARG TRP MET SEQRES 30 A 449 LYS ASP THR ASP SER GLU GLU GLU ILE ARG GLU ALA PHE SEQRES 31 A 449 ARG VAL PHE ASP LYS ASP GLY ASN GLY TYR ILE SER ALA SEQRES 32 A 449 ALA GLU LEU ARG HIS VAL MET THR ASN LEU GLY GLU LYS SEQRES 33 A 449 LEU THR ASP GLU GLU VAL ASP GLU MET ILE ARG GLU ALA SEQRES 34 A 449 ASP ILE ASP GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE SEQRES 35 A 449 VAL GLN MET MET THR ALA LYS
MODRES 3EKH CRO A 224 SER CHROMOPHORE
HET CRO A 224 22 HET GOL A 452 6 HET CA A 453 1 HET CA A 454 1 HET CA A 455 1 HET CA A 456 1
HETNAM CRO {2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4- HETNAM 2 CRO HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 CRO YL}ACETIC ACID HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION
HETSYN CRO PEPTIDE DERIVED CHROMOPHORE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 CRO C15 H17 N3 O5 FORMUL 2 GOL C3 H8 O3 FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *277(H2 O)
HELIX 1 1 SER A 39 SER A 59 1 21 HELIX 2 2 LYS A 69 ASN A 72 5 4 HELIX 3 3 LYS A 161 THR A 167 5 7 HELIX 4 4 PRO A 214 VAL A 219 5 6 HELIX 5 5 VAL A 226 SER A 230 5 5 HELIX 6 6 PRO A 233 HIS A 239 5 7 HELIX 7 7 ASP A 240 ALA A 245 1 6 HELIX 8 8 THR A 308 ASP A 323 1 16 HELIX 9 9 THR A 331 LEU A 342 1 12 HELIX 10 10 THR A 347 GLU A 357 1 11 HELIX 11 11 PHE A 368 LYS A 380 1 13 HELIX 12 12 SER A 384 ASP A 396 1 13 HELIX 13 13 SER A 404 LEU A 415 1 12 HELIX 14 14 THR A 420 ASP A 432 1 13 HELIX 15 15 TYR A 441 MET A 448 1 8
SHEET 1 A12 VAL A 63 ASP A 68 0 SHEET 2 A12 GLY A 73 ASN A 83 -1 O GLY A 73 N ASP A 68 SHEET 3 A12 VAL A 89 PRO A 100 -1 O HIS A 94 N PHE A 78 SHEET 4 A12 TYR A 250 PHE A 258 -1 O GLU A 253 N GLN A 97 SHEET 5 A12 ASN A 263 GLU A 273 -1 O VAL A 270 N TYR A 250 SHEET 6 A12 THR A 276 ILE A 286 -1 O THR A 276 N GLU A 273 SHEET 7 A12 VAL A 169 VAL A 180 1 N GLU A 175 O ILE A 281 SHEET 8 A12 HIS A 183 ASP A 194 -1 O PHE A 185 N GLY A 178 SHEET 9 A12 LYS A 199 CYS A 206 -1 O LYS A 199 N ASP A 194 SHEET 10 A12 HIS A 130 ALA A 140 -1 N MET A 131 O PHE A 204 SHEET 11 A12 HIS A 112 SER A 121 -1 N LYS A 119 O LEU A 134 SHEET 12 A12 VAL A 63 ASP A 68 -1 N ILE A 65 O HIS A 112 SHEET 1 B 2 THR A 329 ILE A 330 0 SHEET 2 B 2 ILE A 366 ASP A 367 -1 O ILE A 366 N ILE A 330 SHEET 1 C 2 TYR A 402 ILE A 403 0 SHEET 2 C 2 VAL A 439 ASN A 440 -1 O VAL A 439 N ILE A 403
LINK C3 CRO A 224 N VAL A 226 1555 1555 1.34 LINK C LEU A 222 N1 CRO A 224 1555 1555 1.35 LINK OD1 ASP A 323 CA CA A 453 1555 1555 2.28 LINK OD1 ASP A 325 CA CA A 453 1555 1555 2.32 LINK OD1 ASP A 327 CA CA A 453 1555 1555 2.32 LINK O THR A 329 CA CA A 453 1555 1555 2.33 LINK OE1 GLU A 334 CA CA A 453 1555 1555 2.52 LINK OE2 GLU A 334 CA CA A 453 1555 1555 2.51 LINK OD2 ASP A 359 CA CA A 454 1555 1555 2.29 LINK OD1 ASP A 361 CA CA A 454 1555 1555 2.47 LINK OD1 ASN A 363 CA CA A 454 1555 1555 2.42 LINK O THR A 365 CA CA A 454 1555 1555 2.38 LINK OD1AASP A 367 CA CA A 454 1555 1555 2.47 LINK OE1 GLU A 370 CA CA A 454 1555 1555 2.36 LINK OE2 GLU A 370 CA CA A 454 1555 1555 2.53 LINK OD2 ASP A 396 CA CA A 455 1555 1555 2.43 LINK OD2 ASP A 398 CA CA A 455 1555 1555 2.69 LINK OD1 ASN A 400 CA CA A 455 1555 1555 2.42 LINK O TYR A 402 CA CA A 455 1555 1555 2.11 LINK OE1 GLU A 407 CA CA A 455 1555 1555 2.57 LINK OE2 GLU A 407 CA CA A 455 1555 1555 2.44 LINK OD1 ASP A 432 CA CA A 456 1555 1555 2.66 LINK OD2 ASP A 434 CA CA A 456 1555 1555 2.71 LINK OD1 ASP A 436 CA CA A 456 1555 1555 2.19 LINK O GLN A 438 CA CA A 456 1555 1555 2.44 LINK OE1 GLU A 443 CA CA A 456 1555 1555 2.60 LINK OE2 GLU A 443 CA CA A 456 1555 1555 2.53 LINK CA CA A 453 O HOH A 536 1555 1555 2.38
CISPEP 1 MET A 246 PRO A 247 0 4.73
SITE 1 AC1 7 ASP A 261 ASP A 287 SER A 320 ASP A 323 SITE 2 AC1 7 GLY A 326 HOH A 476 HOH A 635 SITE 1 AC2 6 ASP A 323 ASP A 325 ASP A 327 THR A 329 SITE 2 AC2 6 GLU A 334 HOH A 536 SITE 1 AC3 6 ASP A 359 ASP A 361 ASN A 363 THR A 365 SITE 2 AC3 6 ASP A 367 GLU A 370 SITE 1 AC4 5 ASP A 396 ASP A 398 ASN A 400 TYR A 402 SITE 2 AC4 5 GLU A 407 SITE 1 AC5 5 ASP A 432 ASP A 434 ASP A 436 GLN A 438 SITE 2 AC5 5 GLU A 443
CRYST1 121.648 121.648 97.327 90.00 90.00 90.00 P 41 21 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 0.008220 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008220 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010275 0.00000