HEADER FLUORESCENT PROTEIN 02-JUN-23 8JLM TITLE CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN SET203EF223DA227 TITLE 2 VARIANT AT PH 4.5 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_TAXID: 6100; SOURCE 4 GENE: GFP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIOIMAGING, SENSOR. GFP, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.C.SHIN REVDAT 3 18-MAR-26 8JLM 1 SEQRES REVDAT 2 17-DEC-25 8JLM 1 JRNL REVDAT 1 04-DEC-24 8JLM 0 JRNL AUTH L.M.LEONG,S.C.SHIN,N.FRANKIV,J.K.RHEE,H.KIM,J.SEONG,J.WOO, JRNL AUTH 2 K.HAN,D.A.STORACE,B.J.BAKER JRNL TITL MODULATING CHROMOPHORE FLEXIBILITY IN GEVIS THROUGH JRNL TITL 2 THREONINE-BASED MOLECULAR SWITCHES REVEALS AN INFLUENCE OF JRNL TITL 3 MEMBRANE CURVATURE ON PROTEIN ACTIVITY. JRNL REF ACS SENS V. 10 8395 2025 JRNL REFN ISSN 2379-3694 JRNL PMID 41123309 JRNL DOI 10.1021/ACSSENSORS.5C01748 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 17592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1760 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 30.8100 - 4.3500 1.00 1355 151 0.1809 0.2364 REMARK 3 2 4.3400 - 3.4500 0.99 1264 141 0.1548 0.1747 REMARK 3 3 3.4500 - 3.0200 0.99 1242 138 0.1667 0.2280 REMARK 3 4 3.0100 - 2.7400 0.99 1230 136 0.1833 0.2454 REMARK 3 5 2.7400 - 2.5400 0.99 1230 138 0.1866 0.2376 REMARK 3 6 2.5400 - 2.3900 0.99 1221 134 0.1828 0.2222 REMARK 3 7 2.3900 - 2.2700 0.99 1223 136 0.2022 0.2736 REMARK 3 8 2.2700 - 2.1700 0.99 1203 134 0.2039 0.2755 REMARK 3 9 2.1700 - 2.0900 0.99 1190 133 0.2192 0.2743 REMARK 3 10 2.0900 - 2.0200 0.98 1204 134 0.2271 0.2571 REMARK 3 11 2.0200 - 1.9600 0.98 1178 130 0.2526 0.2823 REMARK 3 12 1.9600 - 1.9000 0.97 1196 134 0.2789 0.3078 REMARK 3 13 1.9000 - 1.8500 0.91 1096 121 0.2993 0.3584 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1844 REMARK 3 ANGLE : 1.049 2493 REMARK 3 CHIRALITY : 0.065 266 REMARK 3 PLANARITY : 0.010 327 REMARK 3 DIHEDRAL : 6.634 242 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 8JLM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17624 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.35600 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE PH 4.5, 25% (W/V) PEG REMARK 280 1500, 30% (W/V) MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 17.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.61950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.09700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.61950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.09700 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 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 SER A 2 REMARK 465 THR A 230 REMARK 465 HIS 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 171 CD1 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 HIS A 77 2.40 -67.93 REMARK 500 ASP A 103 -159.22 -152.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JLM A 1 238 UNP P42212 GFP_AEQVI 1 238 SEQADV 8JLM LEU A 64 UNP P42212 PHE 64 ENGINEERED MUTATION SEQADV 8JLM CRO A 66 UNP P42212 SER 65 CHROMOPHORE SEQADV 8JLM CRO A 66 UNP P42212 TYR 66 CHROMOPHORE SEQADV 8JLM CRO A 66 UNP P42212 GLY 67 CHROMOPHORE SEQADV 8JLM ARG A 80 UNP P42212 GLN 80 ENGINEERED MUTATION SEQADV 8JLM ASP A 147 UNP P42212 SER 147 ENGINEERED MUTATION SEQADV 8JLM GLN A 149 UNP P42212 ASN 149 ENGINEERED MUTATION SEQADV 8JLM ALA A 163 UNP P42212 VAL 163 ENGINEERED MUTATION SEQADV 8JLM GLY A 175 UNP P42212 SER 175 ENGINEERED MUTATION SEQADV 8JLM PHE A 202 UNP P42212 SER 202 ENGINEERED MUTATION SEQADV 8JLM GLU A 204 UNP P42212 GLN 204 ENGINEERED MUTATION SEQADV 8JLM THR A 206 UNP P42212 ALA 206 ENGINEERED MUTATION SEQADV 8JLM ASP A 223 UNP P42212 PHE 223 ENGINEERED MUTATION SEQRES 1 A 236 MET SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO SEQRES 2 A 236 ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS SEQRES 3 A 236 PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR TYR SEQRES 4 A 236 GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS SEQRES 5 A 236 LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR LEU CRO SEQRES 6 A 236 VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET LYS ARG SEQRES 7 A 236 HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL SEQRES 8 A 236 GLN GLU ARG THR ILE PHE PHE LYS ASP ASP GLY ASN TYR SEQRES 9 A 236 LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU SEQRES 10 A 236 VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU SEQRES 11 A 236 ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN TYR SEQRES 12 A 236 ASN ASP HIS GLN VAL TYR ILE MET ALA ASP LYS GLN LYS SEQRES 13 A 236 ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS ASN ILE SEQRES 14 A 236 GLU ASP GLY GLY VAL GLN LEU ALA ASP HIS TYR GLN GLN SEQRES 15 A 236 ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP SEQRES 16 A 236 ASN HIS TYR LEU PHE THR GLU SER THR LEU SER LYS ASP SEQRES 17 A 236 PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU GLU ASP SEQRES 18 A 236 VAL THR ALA ALA GLY ILE THR HIS GLY MET ASP GLU LEU SEQRES 19 A 236 TYR LYS MODRES 8JLM CRO A 66 SER CHROMOPHORE MODRES 8JLM CRO A 66 TYR CHROMOPHORE MODRES 8JLM CRO A 66 GLY CHROMOPHORE HET CRO A 66 22 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 HETSYN CRO PEPTIDE DERIVED CHROMOPHORE FORMUL 1 CRO C15 H17 N3 O5 FORMUL 2 HOH *138(H2 O) HELIX 1 AA1 GLY A 4 THR A 9 5 6 HELIX 2 AA2 PRO A 56 VAL A 61 5 6 HELIX 3 AA3 VAL A 68 SER 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 HELIX 6 AA6 LYS A 156 ASN A 159 5 4 SHEET 1 AA112 VAL A 11 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 ALA A 227 -1 O LEU A 220 N LEU A 44 SHEET 5 AA112 HIS A 199 SER A 208 -1 N PHE A 202 O THR A 225 SHEET 6 AA112 VAL A 150 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 AA112 GLY A 160 ASN A 170 -1 O LYS A 162 N MET A 153 SHEET 8 AA112 VAL A 176 PRO A 187 -1 O GLN A 177 N HIS A 169 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 VAL A 120 N LYS A 113 SHEET 12 AA112 VAL A 11 VAL A 22 1 N ASP A 21 O GLY A 127 LINK C LEU A 64 N1 CRO A 66 1555 1555 1.31 LINK C3 CRO A 66 N VAL A 68 1555 1555 1.23 CISPEP 1 MET A 88 PRO A 89 0 5.27 CRYST1 35.240 46.194 123.239 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 0.028377 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008114 0.00000 CONECT 458 464 CONECT 464 458 465 CONECT 465 464 466 469 CONECT 466 465 467 468 CONECT 467 466 CONECT 468 466 CONECT 469 465 470 471 CONECT 470 469 474 CONECT 471 469 472 475 CONECT 472 471 473 474 CONECT 473 472 CONECT 474 470 472 478 CONECT 475 471 476 CONECT 476 475 477 486 CONECT 477 476 CONECT 478 474 479 CONECT 479 478 480 481 CONECT 480 479 482 CONECT 481 479 483 CONECT 482 480 484 CONECT 483 481 484 CONECT 484 482 483 485 CONECT 485 484 CONECT 486 476 MASTER 244 0 1 6 12 0 0 6 1945 1 24 19 END