HEADER FLUORESCENT PROTEIN 01-JUN-18 6GO8 TITLE STRUCTURE OF GFPMUT2 CRYSTALLIZED AT PH 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: MUTATIONS: S65A, V68L, S72A;FIRST SIX RESIDUES GSHIGP COMPND 7 DERIVE FROM THE EXPRESSION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_TAXID: 6100; SOURCE 4 GENE: GFP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA BARREL, BIOLUMINESCENCE, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.LOLLI,S.RABONI,E.PASQUALETTO,B.CAMPANINI,A.MOZZARELLI,S.BETTATI, AUTHOR 2 R.BATTISTUTTA REVDAT 3 17-JAN-24 6GO8 1 LINK REVDAT 2 24-APR-19 6GO8 1 JRNL REVDAT 1 19-DEC-18 6GO8 0 JRNL AUTH G.LOLLI,S.RABONI,E.PASQUALETTO,R.BENONI,B.CAMPANINI,L.RONDA, JRNL AUTH 2 A.MOZZARELLI,S.BETTATI,R.BATTISTUTTA JRNL TITL INSIGHT INTO GFPMUT2 PH DEPENDENCE BY SINGLE CRYSTAL JRNL TITL 2 MICROSPECTROPHOTOMETRY AND X-RAY CRYSTALLOGRAPHY. JRNL REF J.PHYS.CHEM.B V. 122 11326 2018 JRNL REFN ISSN 1089-5647 JRNL PMID 30179482 JRNL DOI 10.1021/ACS.JPCB.8B07260 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 25456 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.1471 - 3.4259 0.87 2675 162 0.1421 0.1478 REMARK 3 2 3.4259 - 2.7200 0.90 2622 152 0.1473 0.1609 REMARK 3 3 2.7200 - 2.3763 0.91 2654 158 0.1609 0.1804 REMARK 3 4 2.3763 - 2.1592 0.93 2642 151 0.1534 0.1728 REMARK 3 5 2.1592 - 2.0044 0.94 2721 135 0.1560 0.1629 REMARK 3 6 2.0044 - 1.8863 0.94 2721 113 0.1567 0.1892 REMARK 3 7 1.8863 - 1.7918 0.95 2731 131 0.1619 0.2206 REMARK 3 8 1.7918 - 1.7139 0.97 2734 147 0.1712 0.2064 REMARK 3 9 1.7139 - 1.6479 0.93 2663 144 0.2015 0.2465 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1996 REMARK 3 ANGLE : 1.100 2716 REMARK 3 CHIRALITY : 0.062 301 REMARK 3 PLANARITY : 0.006 346 REMARK 3 DIHEDRAL : 6.017 2052 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.14 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25496 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.648 REMARK 200 RESOLUTION RANGE LOW (A) : 41.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1Q4A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% MPD, PH 6, VAPOR DIFFUSION, 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 16.25200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.24850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.00450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.24850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.25200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.00450 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 TOTAL BURIED SURFACE AREA: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 ILE A -2 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 103 -157.32 -149.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRD A 304 DBREF 6GO8 A 1 238 UNP P42212 GFP_AEQVI 1 238 SEQADV 6GO8 GLY A -5 UNP P42212 EXPRESSION TAG SEQADV 6GO8 SER A -4 UNP P42212 EXPRESSION TAG SEQADV 6GO8 HIS A -3 UNP P42212 EXPRESSION TAG SEQADV 6GO8 ILE A -2 UNP P42212 EXPRESSION TAG SEQADV 6GO8 GLY A -1 UNP P42212 EXPRESSION TAG SEQADV 6GO8 PRO A 0 UNP P42212 EXPRESSION TAG SEQADV 6GO8 PIA A 66 UNP P42212 SER 65 CHROMOPHORE SEQADV 6GO8 PIA A 66 UNP P42212 TYR 66 CHROMOPHORE SEQADV 6GO8 PIA A 66 UNP P42212 GLY 67 CHROMOPHORE SEQADV 6GO8 LEU A 68 UNP P42212 VAL 68 ENGINEERED MUTATION SEQADV 6GO8 ALA A 72 UNP P42212 SER 72 ENGINEERED MUTATION SEQRES 1 A 242 GLY SER HIS ILE GLY PRO MET SER LYS GLY GLU GLU LEU SEQRES 2 A 242 PHE THR GLY VAL VAL PRO ILE LEU VAL GLU LEU ASP GLY SEQRES 3 A 242 ASP VAL ASN GLY HIS LYS PHE SER VAL SER GLY GLU GLY SEQRES 4 A 242 GLU GLY ASP ALA THR TYR GLY LYS LEU THR LEU LYS PHE SEQRES 5 A 242 ILE CYS THR THR GLY LYS LEU PRO VAL PRO TRP PRO THR SEQRES 6 A 242 LEU VAL THR THR PHE PIA LEU GLN CYS PHE ALA ARG TYR SEQRES 7 A 242 PRO ASP HIS MET LYS GLN HIS ASP PHE PHE LYS SER ALA SEQRES 8 A 242 MET PRO GLU GLY TYR VAL GLN GLU ARG THR ILE PHE PHE SEQRES 9 A 242 LYS ASP ASP GLY ASN TYR LYS THR ARG ALA GLU VAL LYS SEQRES 10 A 242 PHE GLU GLY ASP THR LEU VAL ASN ARG ILE GLU LEU LYS SEQRES 11 A 242 GLY ILE ASP PHE LYS GLU ASP GLY ASN ILE LEU GLY HIS SEQRES 12 A 242 LYS LEU GLU TYR ASN TYR ASN SER HIS ASN VAL TYR ILE SEQRES 13 A 242 MET ALA ASP LYS GLN LYS ASN GLY ILE LYS VAL ASN PHE SEQRES 14 A 242 LYS ILE ARG HIS ASN ILE GLU ASP GLY SER VAL GLN LEU SEQRES 15 A 242 ALA ASP HIS TYR GLN GLN ASN THR PRO ILE GLY ASP GLY SEQRES 16 A 242 PRO VAL LEU LEU PRO ASP ASN HIS TYR LEU SER THR GLN SEQRES 17 A 242 SER ALA LEU SER LYS ASP PRO ASN GLU LYS ARG ASP HIS SEQRES 18 A 242 MET VAL LEU LEU GLU PHE VAL THR ALA ALA GLY ILE THR SEQRES 19 A 242 HIS GLY MET ASP GLU LEU TYR LYS MODRES 6GO8 PIA A 66 GLY CHROMOPHORE HET PIA A 66 20 HET MPD A 301 8 HET MRD A 302 8 HET MRD A 303 8 HET MRD A 304 8 HETNAM PIA [(4Z)-2-[(1S)-1-AMINOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5- HETNAM 2 PIA OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 1 PIA C14 H15 N3 O4 FORMUL 2 MPD C6 H14 O2 FORMUL 3 MRD 3(C6 H14 O2) FORMUL 6 HOH *312(H2 O) HELIX 1 AA1 LYS A 3 THR A 9 5 7 HELIX 2 AA2 PRO A 56 VAL A 61 5 6 HELIX 3 AA3 LEU A 68 ALA A 72 5 5 HELIX 4 AA4 PRO A 75 HIS A 81 5 7 HELIX 5 AA5 ASP A 82 ALA A 87 1 6 SHEET 1 AA112 VAL A 12 VAL A 22 0 SHEET 2 AA112 HIS A 25 ASP A 36 -1 O PHE A 27 N GLY A 20 SHEET 3 AA112 LYS A 41 CYS A 48 -1 O ILE A 47 N SER A 30 SHEET 4 AA112 HIS A 217 GLY A 228 -1 O MET A 218 N PHE A 46 SHEET 5 AA112 HIS A 199 SER A 208 -1 N SER A 202 O THR A 225 SHEET 6 AA112 HIS A 148 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 AA112 GLY A 160 ASN A 170 -1 O GLY A 160 N ASP A 155 SHEET 8 AA112 VAL A 176 PRO A 187 -1 O HIS A 181 N PHE A 165 SHEET 9 AA112 TYR A 92 PHE A 100 -1 N VAL A 93 O THR A 186 SHEET 10 AA112 ASN A 105 GLU A 115 -1 O TYR A 106 N ILE A 98 SHEET 11 AA112 THR A 118 ILE A 128 -1 O LYS A 126 N LYS A 107 SHEET 12 AA112 VAL A 12 VAL A 22 1 N ASP A 21 O GLY A 127 LINK C PHE A 64 N1 PIA A 66 1555 1555 1.43 LINK C3 PIA A 66 N LEU A 68 1555 1555 1.43 CISPEP 1 MET A 88 PRO A 89 0 5.19 SITE 1 AC1 8 ARG A 96 THR A 97 PHE A 114 GLY A 116 SITE 2 AC1 8 ASP A 117 TYR A 182 HOH A 515 HOH A 573 SITE 1 AC2 6 TYR A 151 MET A 153 LYS A 162 VAL A 163 SITE 2 AC2 6 ASN A 164 HOH A 470 SITE 1 AC3 8 GLU A 34 LYS A 41 THR A 43 TYR A 151 SITE 2 AC3 8 TYR A 200 HOH A 434 HOH A 448 HOH A 552 SITE 1 AC4 7 PRO A 13 ASN A 149 GLN A 157 SER A 202 SITE 2 AC4 7 GLY A 228 ILE A 229 HOH A 441 CRYST1 32.504 60.009 112.497 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 0.030765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008889 0.00000