HEADER FLUORESCENT PROTEIN 02-OCT-19 6L27 TITLE X-RAY CRYSTAL STRUCTURE OF THE MUTANT GREEN FLUORESCENT PROTEIN 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: THE AMINO ACIDS OF SYG ARE PROCESSED TO CHROMOPHORE AS COMPND 7 COMPND GYS BY POST-TRANSLATIONAL REACTION. 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GFP, MUTANT, RECOMBINANT, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ADACHI,R.SHIMIZU,C.SHIBAZAKI,Y.KAGOTANI,A.OSTERMANN,T.E.SCHRADER REVDAT 3 06-NOV-24 6L27 1 REMARK REVDAT 2 15-NOV-23 6L27 1 LINK ATOM REVDAT 1 01-APR-20 6L27 0 JRNL AUTH C.SHIBAZAKI,R.SHIMIZU,Y.KAGOTANI,A.OSTERMANN,T.E.SCHRADER, JRNL AUTH 2 M.ADACHI JRNL TITL DIRECT OBSERVATION OF THE PROTONATION STATES IN THE MUTANT JRNL TITL 2 GREEN FLUORESCENT PROTEIN. JRNL REF J PHYS CHEM LETT V. 11 492 2020 JRNL REFN ESSN 1948-7185 JRNL PMID 31880458 JRNL DOI 10.1021/ACS.JPCLETT.9B03252 REMARK 2 REMARK 2 RESOLUTION. 0.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 0.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 258108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.124 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 12907 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.050 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.90 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 : 0.015 2201 REMARK 3 ANGLE : 1.587 2989 REMARK 3 CHIRALITY : 0.192 320 REMARK 3 PLANARITY : 0.009 397 REMARK 3 DIHEDRAL : 14.716 855 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 6L27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300014033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.850 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 258331 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.770 REMARK 200 RESOLUTION RANGE LOW (A) : 28.486 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.74000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS 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 (%): 41.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES-NAOD (PD 7.0), 5.0 % W/V PEG REMARK 280 2000 AND 50 MM NDSB, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 25.43750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.38000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.28050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.38000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.43750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.28050 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 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 HE2 HIS A 77 O ILE A 229 1.55 REMARK 500 O THR A 230 O DOD A 301 2.05 REMARK 500 OD1 ASN A 105 O DOD A 302 2.07 REMARK 500 OG1 THR A 225 O DOD A 303 2.11 REMARK 500 O DOD A 580 O DOD A 617 2.11 REMARK 500 O DOD A 582 O DOD A 619 2.13 REMARK 500 O DOD A 302 O DOD A 557 2.16 REMARK 500 O DOD A 432 O DOD A 658 2.17 REMARK 500 O DOD A 304 O DOD A 543 2.18 REMARK 500 O DOD A 503 O DOD A 617 2.19 REMARK 500 O DOD A 323 O DOD A 468 2.19 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 H ASP A 117 HE22 GLN A 204 4455 1.23 REMARK 500 O DOD A 301 O DOD A 422 2665 1.99 REMARK 500 O DOD A 301 O DOD A 588 2665 2.10 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 THR A 50 -107.49 -125.62 REMARK 500 ASP A 103 -159.38 -153.21 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 DOD A 697 DISTANCE = 5.82 ANGSTROMS REMARK 525 DOD A 698 DISTANCE = 6.01 ANGSTROMS REMARK 525 DOD A 699 DISTANCE = 6.05 ANGSTROMS REMARK 525 DOD A 700 DISTANCE = 6.10 ANGSTROMS REMARK 525 DOD A 701 DISTANCE = 6.54 ANGSTROMS REMARK 525 DOD A 702 DISTANCE = 6.88 ANGSTROMS DBREF 6L27 A 4 231 UNP P42212 GFP_AEQVI 4 231 SEQADV 6L27 MET A 3 UNP P42212 INITIATING METHIONINE SEQADV 6L27 SER A 48 UNP P42212 CYS 48 CONFLICT SEQADV 6L27 LEU A 64 UNP P42212 PHE 64 CONFLICT SEQADV 6L27 GYS A 66 UNP P42212 SER 65 CHROMOPHORE SEQADV 6L27 GYS A 66 UNP P42212 TYR 66 CHROMOPHORE SEQADV 6L27 GYS A 66 UNP P42212 GLY 67 CHROMOPHORE SEQADV 6L27 ARG A 80 UNP P42212 GLN 80 CONFLICT SEQADV 6L27 GLN A 159 UNP P42212 ASN 159 CONFLICT SEQADV 6L27 THR A 167 UNP P42212 ILE 167 CONFLICT SEQRES 1 A 227 MET GLY GLU GLU LEU PHE THR GLY VAL VAL PRO ILE LEU SEQRES 2 A 227 VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS PHE SER SEQRES 3 A 227 VAL SER GLY GLU GLY GLU GLY ASP ALA THR TYR GLY LYS SEQRES 4 A 227 LEU THR LEU LYS PHE ILE SER THR THR GLY LYS LEU PRO SEQRES 5 A 227 VAL PRO TRP PRO THR LEU VAL THR THR LEU GYS VAL GLN SEQRES 6 A 227 CYS PHE SER ARG TYR PRO ASP HIS MET LYS ARG HIS ASP SEQRES 7 A 227 PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL GLN GLU SEQRES 8 A 227 ARG THR ILE PHE PHE LYS ASP ASP GLY ASN TYR LYS THR SEQRES 9 A 227 ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU VAL ASN SEQRES 10 A 227 ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU ASP GLY SEQRES 11 A 227 ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN TYR ASN SER SEQRES 12 A 227 HIS ASN VAL TYR ILE MET ALA ASP LYS GLN LYS GLN GLY SEQRES 13 A 227 ILE LYS VAL ASN PHE LYS THR ARG HIS ASN ILE GLU ASP SEQRES 14 A 227 GLY SER VAL GLN LEU ALA ASP HIS TYR GLN GLN ASN THR SEQRES 15 A 227 PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP ASN HIS SEQRES 16 A 227 TYR LEU SER THR GLN SER ALA LEU SER LYS ASP PRO ASN SEQRES 17 A 227 GLU LYS ARG ASP HIS MET VAL LEU LEU GLU PHE VAL THR SEQRES 18 A 227 ALA ALA GLY ILE THR HIS MODRES 6L27 GYS A 66 SER CHROMOPHORE MODRES 6L27 GYS A 66 TYR CHROMOPHORE MODRES 6L27 GYS A 66 GLY CHROMOPHORE HET GYS A 66 34 HETNAM GYS [(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4- HETNAM 2 GYS HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 GYS YL]ACETIC ACID HETSYN GYS CHROMOPHORE (SER-TYR-GLY) FORMUL 1 GYS C14 H15 N3 O5 FORMUL 2 DOD *402(D2 O) HELIX 1 AA1 GLY A 4 THR A 9 5 6 HELIX 2 AA2 ALA A 37 TYR A 39 5 3 HELIX 3 AA3 PRO A 56 VAL A 61 5 6 HELIX 4 AA4 VAL A 68 SER A 72 5 5 HELIX 5 AA5 PRO A 75 HIS A 81 5 7 HELIX 6 AA6 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 SER A 48 -1 O LYS A 41 N ASP A 36 SHEET 4 AA112 HIS A 217 ALA A 227 -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 ALA A 154 -1 N ILE A 152 O HIS A 199 SHEET 7 AA112 ILE A 161 ASN A 170 -1 O LYS A 162 N MET A 153 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 VAL A 120 N LYS A 113 SHEET 12 AA112 VAL A 12 VAL A 22 1 N ASP A 21 O GLY A 127 LINK C LEU A 64 N1 GYS A 66 1555 1555 1.35 LINK C3 GYS A 66 N VAL A 68 1555 1555 1.33 CISPEP 1 MET A 88 PRO A 89 0 9.48 CRYST1 50.875 62.561 68.760 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 0.019656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014543 0.00000