HEADER DE NOVO PROTEIN 28-JAN-24 8Y33 TITLE A NEAR-INFRARED FLUORESCENT PROTEIN OF DE NOVO BACKBONE DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEAR-INFRARED FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO BACKBONE DESIGN, MONOMERIZATION, NEAR-INFRARED FLUORESCENT KEYWDS 2 PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.HU,Y.XU REVDAT 3 01-MAY-24 8Y33 1 JRNL REVDAT 2 17-APR-24 8Y33 1 JRNL REVDAT 1 28-FEB-24 8Y33 0 JRNL AUTH X.HU,Y.XU,J.YI,C.WANG,Z.ZHU,T.YUE,H.ZHANG,X.WANG,F.WU,L.XUE, JRNL AUTH 2 L.BAI,H.LIU,Q.CHEN JRNL TITL USING PROTEIN DESIGN AND DIRECTED EVOLUTION TO MONOMERIZE A JRNL TITL 2 BRIGHT NEAR-INFRARED FLUORESCENT PROTEIN. JRNL REF ACS SYNTH BIOL V. 13 1177 2024 JRNL REFN ESSN 2161-5063 JRNL PMID 38552148 JRNL DOI 10.1021/ACSSYNBIO.3C00643 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 5854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 278 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 34.6900 - 3.6800 0.98 2807 167 0.1854 0.2103 REMARK 3 2 3.6500 - 2.9000 0.95 2769 111 0.2224 0.3236 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.28 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 : 0.002 1551 REMARK 3 ANGLE : 0.694 2090 REMARK 3 CHIRALITY : 0.032 218 REMARK 3 PLANARITY : 0.003 263 REMARK 3 DIHEDRAL : 11.136 215 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3735 56.5301 -0.9499 REMARK 3 T TENSOR REMARK 3 T11: 0.2487 T22: 0.1363 REMARK 3 T33: 0.1599 T12: -0.0731 REMARK 3 T13: 0.0173 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 3.7912 L22: 3.0700 REMARK 3 L33: 1.1236 L12: -1.1890 REMARK 3 L13: 1.1413 L23: -0.4513 REMARK 3 S TENSOR REMARK 3 S11: 0.1664 S12: 0.4417 S13: 0.6335 REMARK 3 S21: -0.4831 S22: -0.2042 S23: -0.1911 REMARK 3 S31: -0.2543 S32: 0.2638 S33: -0.0808 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 165 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.5520 53.2648 15.1140 REMARK 3 T TENSOR REMARK 3 T11: 0.1320 T22: 0.1242 REMARK 3 T33: 0.1743 T12: -0.0560 REMARK 3 T13: 0.0199 T23: 0.0263 REMARK 3 L TENSOR REMARK 3 L11: 2.5416 L22: 0.9171 REMARK 3 L33: 3.5583 L12: -1.0629 REMARK 3 L13: 1.3769 L23: -0.8892 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: -0.0869 S13: -0.0220 REMARK 3 S21: 0.0388 S22: 0.0279 S23: -0.0373 REMARK 3 S31: -0.2093 S32: 0.2643 S33: -0.0193 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 166 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.7145 49.0660 20.1330 REMARK 3 T TENSOR REMARK 3 T11: 0.1139 T22: 0.2346 REMARK 3 T33: 0.1510 T12: 0.0315 REMARK 3 T13: 0.0704 T23: 0.0358 REMARK 3 L TENSOR REMARK 3 L11: 0.7722 L22: 3.4985 REMARK 3 L33: 3.4635 L12: 1.4552 REMARK 3 L13: -0.1511 L23: -0.8725 REMARK 3 S TENSOR REMARK 3 S11: -0.1529 S12: 0.0393 S13: -0.0281 REMARK 3 S21: 0.3735 S22: 0.1374 S23: -0.1220 REMARK 3 S31: -0.3010 S32: -0.0453 S33: -0.0669 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 8Y33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978510 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6001 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, 0.1 M TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.79400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.89700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.84550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 6.94850 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.74250 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 35 CG CD OE1 OE2 REMARK 470 GLU A 180 CG CD OE1 OE2 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 SG CYS A 127A CAC V8U A 301 1.81 REMARK 500 NZ LYS A 147 OE2 GLU A 151 2.06 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 ASN A 92 34.11 -99.02 REMARK 500 HIS A 213 35.16 -82.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Y33 A 31 214 PDB 8Y33 8Y33 31 214 SEQRES 1 A 184 GLY ARG GLY SER GLU ASP PHE GLN TYR ALA ILE ASP MET SEQRES 2 A 184 PHE LYS LYS PHE ILE GLU GLU ALA ALA ALA SER MET GLY SEQRES 3 A 184 PRO GLU ALA VAL LYS TYR ALA LYS GLU PHE LEU LYS LEU SEQRES 4 A 184 LEU LYS GLU TYR HIS LYS ASN GLY ILE ASN ASN ARG LEU SEQRES 5 A 184 LEU LYS ILE ALA LEU LEU LEU LEU ARG ASN GLN LYS LYS SEQRES 6 A 184 ILE VAL ASP LYS ALA SER GLN ASP LEU TRP ARG ARG HIS SEQRES 7 A 184 PRO GLU LEU ILE ALA PRO GLY GLY ILE ALA PHE SER GLN SEQRES 8 A 184 ARG ASP ARG ALA LEU CYS LEU ARG ASP TYR GLY TRP PHE SEQRES 9 A 184 LEU ILE LEU ILE VAL MET CYS LEU VAL SER GLY ASP LYS SEQRES 10 A 184 GLY PRO ILE GLU LYS ILE GLY LEU LYS CYS ILE ARG GLU SEQRES 11 A 184 MET TYR ASN SER LEU GLY VAL VAL PRO ALA MET MET GLU SEQRES 12 A 184 SER ILE ARG CYS LEU LYS GLU ALA SER LEU SER LEU LEU SEQRES 13 A 184 ASP GLU GLU ASP ALA ASN GLU THR ALA PRO TYR PHE ASP SEQRES 14 A 184 TYR ILE ILE LYS ALA MET SER LEU GLU HIS HIS HIS HIS SEQRES 15 A 184 HIS HIS HET V8U A 301 43 HETNAM V8U 3-[5-[(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YL) HETNAM 2 V8U METHYL]-2-[[5-[(3-ETHYL-4-METHYL-5-OXIDANYLIDENE- HETNAM 3 V8U PYRROL-2-YL)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4- HETNAM 4 V8U METHYL-1~{H}-PYRROL-2-YL]METHYL]-4-METHYL-1~{H}- HETNAM 5 V8U PYRROL-3-YL]PROPANOIC ACID FORMUL 2 V8U C33 H38 N4 O6 HELIX 1 AA1 ASP A 36 GLY A 56 1 21 HELIX 2 AA2 GLY A 56 LYS A 75 1 20 HELIX 3 AA3 ASN A 79 ASN A 92 1 14 HELIX 4 AA4 ASN A 92 HIS A 108 1 17 HELIX 5 AA5 PRO A 109 ILE A 112 5 4 HELIX 6 AA6 SER A 120 GLY A 145 1 26 HELIX 7 AA7 LYS A 147 GLY A 166 1 20 HELIX 8 AA8 VAL A 168 MET A 172 5 5 HELIX 9 AA9 GLU A 173 SER A 184 1 12 HELIX 10 AB1 ASP A 187 HIS A 211 1 25 CRYST1 105.987 105.987 41.691 90.00 90.00 120.00 P 65 6 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 0.009435 0.005447 0.000000 0.00000 SCALE2 0.000000 0.010895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023986 0.00000