HEADER FLUORESCENT PROTEIN 02-NOV-11 3UG0 TITLE CRYSTAL STRUCTURE OF A TRP-LESS GREEN FLUORESCENT PROTEIN TRANSLATED TITLE 2 BY THE SIMPLIFIED GENETIC CODE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-229; COMPND 5 ENGINEERED: YES; COMPND 6 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: CELL-FREE SYNTHESIS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: JELLYFISH; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGFP; SOURCE 9 OTHER_DETAILS: ESCHERICHIA COLI BL21(DE3) KEYWDS GREEN FLUORESCENT PROTEIN, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.KAWAHARA-KOBAYASHI,Y.ARAISO,T.MATSUDA,S.YOKOYAMA,T.KIGAWA,O.NUREKI, AUTHOR 2 D.KIGA REVDAT 5 06-DEC-23 3UG0 1 REMARK REVDAT 4 01-NOV-23 3UG0 1 SEQADV LINK REVDAT 3 24-JAN-18 3UG0 1 REMARK REVDAT 2 17-JUL-13 3UG0 1 JRNL REVDAT 1 17-OCT-12 3UG0 0 JRNL AUTH A.KAWAHARA-KOBAYASHI,A.MASUDA,Y.ARAISO,Y.SAKAI,A.KOHDA, JRNL AUTH 2 M.UCHIYAMA,S.ASAMI,T.MATSUDA,R.ISHITANI,N.DOHMAE,S.YOKOYAMA, JRNL AUTH 3 T.KIGAWA,O.NUREKI,D.KIGA JRNL TITL SIMPLIFICATION OF THE GENETIC CODE: RESTRICTED DIVERSITY OF JRNL TITL 2 GENETICALLY ENCODED AMINO ACIDS. JRNL REF NUCLEIC ACIDS RES. V. 40 10576 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22909996 JRNL DOI 10.1093/NAR/GKS786 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 665 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 33.7049 - 3.5776 1.00 2695 145 0.1595 0.2096 REMARK 3 2 3.5776 - 2.8401 1.00 2571 131 0.1799 0.2377 REMARK 3 3 2.8401 - 2.4812 1.00 2554 113 0.1908 0.2882 REMARK 3 4 2.4812 - 2.2544 1.00 2499 134 0.1927 0.2502 REMARK 3 5 2.2544 - 2.0929 0.97 2453 142 0.2458 0.3104 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 41.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36750 REMARK 3 B22 (A**2) : -0.07490 REMARK 3 B33 (A**2) : 0.44240 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 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 : 0.007 1842 REMARK 3 ANGLE : 1.339 2505 REMARK 3 CHIRALITY : 0.074 277 REMARK 3 PLANARITY : 0.005 329 REMARK 3 DIHEDRAL : 14.423 675 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 3UG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13473 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.38700 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: MOLREP REMARK 200 STARTING MODEL: 1MEA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 20000, 100MM MES (PH6.5), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 25.89200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.70050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.70050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.89200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.52500 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 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 GLU A 5 CG CD OE1 OE2 REMARK 470 LYS A 52 CD CE NZ REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 126 CD CE NZ REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 ASP A 133 CG OD1 OD2 REMARK 470 LYS A 156 CD CE NZ REMARK 470 GLN A 157 CG CD OE1 NE2 REMARK 470 ILE A 229 CG1 CG2 CD1 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 OG1 THR A 225 O HOH A 363 2.16 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 ASP A 103 -159.32 -164.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UFZ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE SER65 IS MUTATED TO GLY. RESIDUES GLY65, TYR66 AND GLY67 REMARK 999 CONSTITUTE THE CHROMOPHORE CRO. DBREF 3UG0 A 2 229 UNP P42212 GFP_AEQVI 2 229 SEQADV 3UG0 LYS A 1 UNP P42212 EXPRESSION TAG SEQADV 3UG0 ALA A 9 UNP P42212 THR 9 ENGINEERED MUTATION SEQADV 3UG0 PHE A 57 UNP P42212 TRP 57 ENGINEERED MUTATION SEQADV 3UG0 CRO A 66 UNP P42212 SER 65 SEE REMARK 999 SEQADV 3UG0 CRO A 66 UNP P42212 TYR 66 SEE REMARK 999 SEQADV 3UG0 CRO A 66 UNP P42212 GLY 67 SEE REMARK 999 SEQADV 3UG0 ARG A 80 UNP P42212 GLN 80 ENGINEERED MUTATION SEQADV 3UG0 SER A 99 UNP P42212 PHE 99 ENGINEERED MUTATION SEQADV 3UG0 THR A 153 UNP P42212 MET 153 ENGINEERED MUTATION SEQADV 3UG0 ALA A 163 UNP P42212 VAL 163 ENGINEERED MUTATION SEQADV 3UG0 CYS A 200 UNP P42212 TYR 200 ENGINEERED MUTATION SEQADV 3UG0 THR A 205 UNP P42212 SER 205 ENGINEERED MUTATION SEQADV 3UG0 VAL A 206 UNP P42212 ALA 206 ENGINEERED MUTATION SEQRES 1 A 227 LYS SER LYS GLY GLU GLU LEU PHE ALA GLY VAL VAL PRO SEQRES 2 A 227 ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS SEQRES 3 A 227 PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR TYR SEQRES 4 A 227 GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS SEQRES 5 A 227 LEU PRO VAL PRO PHE PRO THR LEU VAL THR THR LEU CRO SEQRES 6 A 227 VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET LYS ARG SEQRES 7 A 227 HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL SEQRES 8 A 227 GLN GLU ARG THR ILE SER PHE LYS ASP ASP GLY ASN TYR SEQRES 9 A 227 LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU SEQRES 10 A 227 VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU SEQRES 11 A 227 ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN TYR SEQRES 12 A 227 ASN SER HIS ASN VAL TYR ILE THR ALA ASP LYS GLN LYS SEQRES 13 A 227 ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS ASN ILE SEQRES 14 A 227 GLU ASP GLY SER VAL GLN LEU ALA ASP HIS TYR GLN GLN SEQRES 15 A 227 ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP SEQRES 16 A 227 ASN HIS CYS LEU SER THR GLN THR VAL LEU SER LYS ASP SEQRES 17 A 227 PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU GLU PHE SEQRES 18 A 227 VAL THR ALA ALA GLY ILE MODRES 3UG0 CRO A 66 GLY MODRES 3UG0 CRO A 66 TYR MODRES 3UG0 CRO A 66 GLY 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 *74(H2 O) HELIX 1 1 SER A 2 PHE A 8 1 7 HELIX 2 2 ALA A 37 TYR A 39 5 3 HELIX 3 3 PRO A 56 VAL A 61 5 6 HELIX 4 4 VAL A 68 SER A 72 5 5 HELIX 5 5 PRO A 75 HIS A 81 5 7 HELIX 6 6 ASP A 82 ALA A 87 1 6 HELIX 7 7 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 VAL A 29 N LEU A 18 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 VAL A 206 O LEU A 221 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 GLY A 160 N ASP A 155 SHEET 8 A12 VAL A 176 PRO A 187 -1 O GLN A 177 N HIS A 169 SHEET 9 A12 TYR A 92 PHE A 100 -1 N VAL A 93 O THR A 186 SHEET 10 A12 ASN A 105 GLU A 115 -1 O TYR A 106 N ILE A 98 SHEET 11 A12 THR A 118 ILE A 128 -1 O VAL A 120 N LYS A 113 SHEET 12 A12 VAL A 12 VAL A 22 1 N ASP A 21 O GLY A 127 LINK C LEU A 64 N1 CRO A 66 1555 1555 1.34 LINK C3 CRO A 66 N VAL A 68 1555 1555 1.33 CISPEP 1 MET A 88 PRO A 89 0 3.69 CRYST1 51.784 63.050 67.401 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 0.019311 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014837 0.00000