PDB Short entry for 3DQE HEADER LUMINESCENT PROTEIN 09-JUL-08 3DQE TITLE STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 TITLE 2 ATMOSPHERES NUMBER 1: STRUCTURE 11 IN A SERIES OF 26 HIGH PRESSURE TITLE 3 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_COMMON: JELLYFISH; SOURCE 4 ORGANISM_TAXID: 6100; SOURCE 5 GENE: GFP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS YELLOW FLUORESCENT PROTEIN, BETA BARREL, CHROMOPHORE, FLUORESCENT KEYWDS 2 PROTEIN, HIGH PRESSURE, LUMINESCENCE, PHOTOPROTEIN, LUMINESCENT KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.BARSTOW,C.U.KIM REVDAT 5 15-NOV-23 3DQE 1 REMARK REVDAT 4 30-AUG-23 3DQE 1 REMARK REVDAT 3 20-OCT-21 3DQE 1 SEQADV LINK REVDAT 2 24-FEB-09 3DQE 1 VERSN REVDAT 1 23-SEP-08 3DQE 0 JRNL AUTH B.BARSTOW,N.ANDO,C.U.KIM,S.M.GRUNER JRNL TITL ALTERATION OF CITRINE STRUCTURE BY HYDROSTATIC PRESSURE JRNL TITL 2 EXPLAINS THE ACCOMPANYING SPECTRAL SHIFT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 13362 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18768811 JRNL DOI 10.1073/PNAS.0802252105 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.U.KIM,R.KAPFER,S.M.GRUNER REMARK 1 TITL HIGH-PRESSURE COOLING OF PROTEIN CRYSTALS WITHOUT REMARK 1 TITL 2 CRYOPROTECTANTS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 61 881 2005 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15983410 REMARK 1 DOI 10.1107/S090744490500836X REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 78.3 REMARK 3 NUMBER OF REFLECTIONS : 32312 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1719 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) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 115 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 3.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.4530 REMARK 3 BIN FREE R VALUE SET COUNT : 2 REMARK 3 BIN FREE R VALUE : 0.6220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 312 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.10000 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.087 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1896 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2559 ; 2.400 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 7.254 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;31.826 ;25.109 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;16.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;12.067 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 272 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1451 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 972 ; 0.293 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1240 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 230 ; 0.187 ; 0.200 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): 42 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.169 ; 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): 1187 ; 2.184 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1841 ; 2.358 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 829 ; 4.552 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 718 ; 6.054 ; 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. THIS STRUCTURE IS REFINED SLIGHTLY REMARK 3 DIFFERENTLY FROM THE CORRESPONDING STRUCTURE USED FOR ANALYSIS REMARK 3 IN THE PRIMARY CITATION (BARSTOW ET AL.). HOWEVER, ANALYSIS OF REMARK 3 THE DEFORMATION MOTION OF THE CHROMOPHORE UNDER PRESSURE IN THIS REMARK 3 SEQUENCE OF DEPOSITED STRUCTURES PRODUCES AN IDENTICAL REMARK 3 DEFORMATION TREND. FOR COPIES OF THE STRUCTURES AS USED IN THE REMARK 3 ANALYSIS IN THE PRIMARY CITATION PLEASE CONTACT THE AUTHORS. REMARK 4 REMARK 4 3DQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048358. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34048 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 39.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30600 REMARK 200 R SYM FOR SHELL (I) : 0.30600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: PDB ENTRY 1HUY WITH RESIDUE 80 MUTATED TO REMARK 200 GLUTAMINE REMARK 200 REMARK 200 REMARK: CRYSTAL STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN REMARK 200 CITRINE FROZEN AT 1250 ATMOSPHERES. STRUCTURE 11 OF 26 IN A REMARK 200 SERIES OF HIGH PRESSURE STRUCTURES. CRYSTAL WAS HIGH PRESSURE REMARK 200 CRYO-COOLED AT 1250 ATMOSPHERES IN HELIUM GAS. CRYSTAL REMARK 200 TEMPERATURE WAS MAINTAINED BELOW 100 K PRIOR TO DATA COLLECTION REMARK 200 AT AMBIENT PRESSURE AND 100 K. HIGH PRESSURE CRYO-COOLING REMARK 200 PROCEDURE IS DESCRIBED IN SECONDARY CITATION 1 (KIM ET AL., ACTA REMARK 200 CRYST. D61:881-890). STRUCTURE REFERRED TO AS CITRINE1250_1 IN REMARK 200 PRIMARY CITATION (BARSTOW ET AL.). REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GROWN BY SEEDING USING A SEED REMARK 280 BEAD (HR2-320, HAMPTON RESEARCH) IN 5% PEG 3350, 50 MM NA REMARK 280 ACETATE, 50 MM NH4 ACETATE, PH 5.0. CRYSTALS WERE GROWN AT 4 DEG REMARK 280 C AND AT AMBIENT PRESSURE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 GLY A -4 REMARK 465 ASP A -3 REMARK 465 LEU A 231 REMARK 465 GLY A 232 REMARK 465 MET A 233 REMARK 465 ASP A 234 REMARK 465 GLU A 235 REMARK 465 LEU A 236 REMARK 465 TYR A 237 REMARK 465 LYS A 238 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 CB ASP A 19 O HOH A 532 2.14 REMARK 500 OD2 ASP A 102 O HOH A 531 2.16 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 GLU A 90 CG GLU A 90 CD 0.108 REMARK 500 TYR A 106 CD1 TYR A 106 CE1 0.118 REMARK 500 GLU A 124 CG GLU A 124 CD 0.104 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 19 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 LEU A 68 CB - CG - CD1 ANGL. DEV. = -10.6 DEGREES REMARK 500 ASP A 133 CB - CG - OD1 ANGL. DEV. = 5.9 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 GLU A 132 -54.37 -23.18 REMARK 500 ILE A 136 -67.29 -90.25 REMARK 500 SER A 175 -166.75 -78.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HUY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CITRINE, AN IMPROVED YELLOW VARIANT OF GREEN REMARK 900 FLUORESCENT PROTEIN REMARK 900 RELATED ID: 1YFP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP, P21212 SPACE REMARK 900 GROUP REMARK 900 RELATED ID: 2YFP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP, P212121 SPACE REMARK 900 GROUP REMARK 900 RELATED ID: 1F0B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT REMARK 900 YFP-H148Q REMARK 900 RELATED ID: 1F09 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT REMARK 900 YFP-H148Q WITH TWO BOUND IODIDES REMARK 900 RELATED ID: 3DPW RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1 REMARK 900 ATMOSPHERE NUMBER 1: STRUCTURE 1 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DPX RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 5000 REMARK 900 ATMOSPHERES: STRUCTURE 26 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES REMARK 900 RELATED ID: 3DPZ RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 4000 REMARK 900 ATMOSPHERES NUMBER 3: STRUCTURE 25 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ1 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 4000 REMARK 900 ATMOSPHERES NUMBER 2: STRUCTURE 24 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ2 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 4000 REMARK 900 ATMOSPHERES NUMBER 1: STRUCTURE 23 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ3 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 2500 REMARK 900 ATMOSPHERES: STRUCTURE 22 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES REMARK 900 RELATED ID: 3DQ4 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 2000 REMARK 900 ATMOSPHERES NUMBER 2: STRUCTURE 20 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ5 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1960 REMARK 900 ATMOSPHERES: STRUCTURE 19 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES REMARK 900 RELATED ID: 3DQ6 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1920 REMARK 900 ATMOSPHERES NUMBER 2: STRUCTURE 18 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ7 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1920 REMARK 900 ATMOSPHERES NUMBER 1: STRUCTURE 17 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ8 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1500 REMARK 900 ATMOSPHERES NUMBER 2: STRUCTURE 16 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQ9 RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1500 REMARK 900 ATMOSPHERES NUMBER 1: STRUCTURE 15 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQA RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 REMARK 900 ATMOSPHERES NUMBER 4: STRUCTURE 14 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQC RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 REMARK 900 ATMOSPHERES NUMBER 3: STRUCTURE 13 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQD RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 REMARK 900 ATMOSPHERES NUMBER 2: STRUCTURE 12 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQF RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 REMARK 900 ATMOSPHERES NUMBER 6: STRUCTURE 10 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQH RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 REMARK 900 ATMOSPHERES NUMBER 5: STRUCTURE 9 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQI RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 REMARK 900 ATMOSPHERES NUMBER 4: STRUCTURE 8 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQJ RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 REMARK 900 ATMOSPHERES NUMBER 3: STRUCTURE 7 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQK RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 REMARK 900 ATMOSPHERES NUMBER 2: STRUCTURE 6 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQL RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 REMARK 900 ATMOSPHERES NUMBER 1: STRUCTURE 5 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQM RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 750 REMARK 900 ATMOSPHERES: STRUCTURE 4 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES REMARK 900 RELATED ID: 3DQN RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 500 REMARK 900 ATMOSPHERES: STRUCTURE 3 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES REMARK 900 RELATED ID: 3DQO RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1 REMARK 900 ATMOSPHERE NUMBER 2: STRUCTURE 2 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 900 RELATED ID: 3DQU RELATED DB: PDB REMARK 900 STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 2000 REMARK 900 ATMOSPHERES NUMBER 1: STRUCTURE 20 IN A SERIES OF 26 HIGH PRESSURE REMARK 900 STRUCTURES REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. REMARK 999 RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE REMARK 999 CHROMOPHORE CR2 66. DBREF 3DQE A 2 238 UNP P42212 GFP_AEQVI 2 238 SEQADV 3DQE GLY A -4 UNP P42212 EXPRESSION TAG SEQADV 3DQE ASP A -3 UNP P42212 EXPRESSION TAG SEQADV 3DQE ASP A -2 UNP P42212 EXPRESSION TAG SEQADV 3DQE PRO A -1 UNP P42212 EXPRESSION TAG SEQADV 3DQE MET A 0 UNP P42212 EXPRESSION TAG SEQADV 3DQE VAL A 1 UNP P42212 EXPRESSION TAG SEQADV 3DQE CR2 A 66 UNP P42212 SER 65 CHROMOPHORE SEQADV 3DQE CR2 A 66 UNP P42212 TYR 66 CHROMOPHORE SEQADV 3DQE CR2 A 66 UNP P42212 GLY 67 CHROMOPHORE SEQADV 3DQE LEU A 68 UNP P42212 VAL 68 ENGINEERED MUTATION SEQADV 3DQE MET A 69 UNP P42212 GLN 69 ENGINEERED MUTATION SEQADV 3DQE ALA A 72 UNP P42212 SER 72 ENGINEERED MUTATION SEQADV 3DQE TYR A 203 UNP P42212 THR 203 ENGINEERED MUTATION SEQADV 3DQE LEU A 231 UNP P42212 HIS 231 ENGINEERED MUTATION SEQRES 1 A 241 GLY ASP ASP PRO MET VAL SER LYS GLY GLU GLU LEU PHE SEQRES 2 A 241 THR GLY VAL VAL PRO ILE LEU VAL GLU LEU ASP GLY ASP SEQRES 3 A 241 VAL ASN GLY HIS LYS PHE SER VAL SER GLY GLU GLY GLU SEQRES 4 A 241 GLY ASP ALA THR TYR GLY LYS LEU THR LEU LYS PHE ILE SEQRES 5 A 241 CYS THR THR GLY LYS LEU PRO VAL PRO TRP PRO THR LEU SEQRES 6 A 241 VAL THR THR PHE CR2 LEU MET CYS PHE ALA ARG TYR PRO SEQRES 7 A 241 ASP HIS MET LYS GLN HIS ASP PHE PHE LYS SER ALA MET SEQRES 8 A 241 PRO GLU GLY TYR VAL GLN GLU ARG THR ILE PHE PHE LYS SEQRES 9 A 241 ASP ASP GLY ASN TYR LYS THR ARG ALA GLU VAL LYS PHE SEQRES 10 A 241 GLU GLY ASP THR LEU VAL ASN ARG ILE GLU LEU LYS GLY SEQRES 11 A 241 ILE ASP PHE LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS SEQRES 12 A 241 LEU GLU TYR ASN TYR ASN SER HIS ASN VAL TYR ILE MET SEQRES 13 A 241 ALA ASP LYS GLN LYS ASN GLY ILE LYS VAL ASN PHE LYS SEQRES 14 A 241 ILE ARG HIS ASN ILE GLU ASP GLY SER VAL GLN LEU ALA SEQRES 15 A 241 ASP HIS TYR GLN GLN ASN THR PRO ILE GLY ASP GLY PRO SEQRES 16 A 241 VAL LEU LEU PRO ASP ASN HIS TYR LEU SER TYR GLN SER SEQRES 17 A 241 ALA LEU SER LYS ASP PRO ASN GLU LYS ARG ASP HIS MET SEQRES 18 A 241 VAL LEU LEU GLU PHE VAL THR ALA ALA GLY ILE THR LEU SEQRES 19 A 241 GLY MET ASP GLU LEU TYR LYS MODRES 3DQE CR2 A 66 GLY MODRES 3DQE CR2 A 66 TYR MODRES 3DQE CR2 A 66 GLY HET CR2 A 66 19 HETNAM CR2 {(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]- HETNAM 2 CR2 5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID HETSYN CR2 CHROMOPHORE (GLY-TYR-GLY) FORMUL 1 CR2 C13 H13 N3 O4 FORMUL 2 HOH *312(H2 O) HELIX 1 1 ASP A -2 THR A 9 1 12 HELIX 2 2 PRO A 56 VAL A 61 5 6 HELIX 3 3 LEU A 68 ALA A 72 5 5 HELIX 4 4 PRO A 75 HIS A 81 5 7 HELIX 5 5 ASP A 82 ALA A 87 1 6 HELIX 6 6 LYS A 156 ASN A 159 5 4 SHEET 1 A12 VAL A 12 VAL A 22 0 SHEET 2 A12 HIS A 25 ASP A 36 -1 O PHE A 27 N GLY A 20 SHEET 3 A12 LYS A 41 CYS A 48 -1 O ILE A 47 N SER A 30 SHEET 4 A12 HIS A 217 ALA A 227 -1 O MET A 218 N PHE A 46 SHEET 5 A12 HIS A 199 SER A 208 -1 N SER A 202 O THR A 225 SHEET 6 A12 HIS A 148 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 A12 GLY A 160 ASN A 170 -1 O LYS A 162 N MET A 153 SHEET 8 A12 VAL A 176 PRO A 187 -1 O HIS A 181 N PHE A 165 SHEET 9 A12 TYR A 92 PHE A 100 -1 N GLU A 95 O GLN A 184 SHEET 10 A12 ASN A 105 GLU A 115 -1 O VAL A 112 N TYR A 92 SHEET 11 A12 THR A 118 ILE A 128 -1 O THR A 118 N GLU A 115 SHEET 12 A12 VAL A 12 VAL A 22 1 N ASP A 21 O GLY A 127 LINK C PHE A 64 N1 CR2 A 66 1555 1555 1.34 LINK C3 CR2 A 66 N LEU A 68 1555 1555 1.27 CISPEP 1 MET A 88 PRO A 89 0 2.17 CRYST1 51.360 62.800 71.000 90.00 90.00 90.00 P 21 21 21 4 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 0.019470 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014085 0.00000