HEADER ANTITUMOR PROTEIN-IMMUNE SYSTEM 28-FEB-23 8IJS TITLE ANTI-VEGF NANOBODY MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-VEGF NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTI-VEGF, NANOBODY, ANTITUMOR PROTEIN, ANTITUMOR PROTEIN-IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR F.QIAN,S.Q.ZHU REVDAT 1 27-DEC-23 8IJS 0 JRNL AUTH S.ZHU,S.FAN,T.TANG,J.HUANG,H.ZHOU,C.HUANG,Y.CHEN,F.QIAN JRNL TITL POLYMORPHIC NANOBODY CRYSTALS AS LONG-ACTING INTRAVITREAL JRNL TITL 2 THERAPY FOR WET AGE-RELATED MACULAR DEGENERATION. JRNL REF BIOENG TRANSL MED V. 8 10523 2023 JRNL REFN ISSN 2380-6761 JRNL PMID 38023710 JRNL DOI 10.1002/BTM2.10523 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.1.3 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 9121 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) : 0.201 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 913 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 20.1700 - 3.3500 1.00 1275 142 0.1847 0.1930 REMARK 3 2 3.3500 - 2.6600 1.00 1196 133 0.1980 0.2119 REMARK 3 3 2.6600 - 2.3200 1.00 1192 133 0.2210 0.2446 REMARK 3 4 2.3200 - 2.1100 1.00 1165 129 0.2031 0.2488 REMARK 3 5 2.1100 - 1.9600 1.00 1164 130 0.2244 0.2709 REMARK 3 6 1.9600 - 1.8400 1.00 1168 129 0.2474 0.3050 REMARK 3 7 1.8400 - 1.7520 0.90 1048 117 0.2766 0.3504 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.070 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 : 0.006 917 REMARK 3 ANGLE : 0.961 1236 REMARK 3 CHIRALITY : 0.056 131 REMARK 3 PLANARITY : 0.010 158 REMARK 3 DIHEDRAL : 6.416 132 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 4 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2035 -11.1161 -15.5529 REMARK 3 T TENSOR REMARK 3 T11: 0.2945 T22: 0.2592 REMARK 3 T33: 0.2457 T12: -0.0233 REMARK 3 T13: 0.0125 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 6.5192 L22: 5.2612 REMARK 3 L33: 5.7786 L12: 0.4276 REMARK 3 L13: 2.4660 L23: -0.4349 REMARK 3 S TENSOR REMARK 3 S11: 0.0911 S12: 0.6486 S13: -0.3296 REMARK 3 S21: -0.4754 S22: 0.2104 S23: 0.3658 REMARK 3 S31: 0.4259 S32: 0.1569 S33: -0.2018 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5512 -0.5809 -16.6964 REMARK 3 T TENSOR REMARK 3 T11: 0.2483 T22: 0.2813 REMARK 3 T33: 0.3356 T12: 0.0157 REMARK 3 T13: -0.0056 T23: 0.0302 REMARK 3 L TENSOR REMARK 3 L11: 5.8821 L22: 7.1796 REMARK 3 L33: 2.1203 L12: -0.3042 REMARK 3 L13: 0.5365 L23: -1.0452 REMARK 3 S TENSOR REMARK 3 S11: -0.2154 S12: -0.2246 S13: 0.2743 REMARK 3 S21: 0.2152 S22: 0.4402 S23: -0.2259 REMARK 3 S31: -0.3833 S32: 0.0553 S33: -0.6915 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 68 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8929 -6.3735 -16.3192 REMARK 3 T TENSOR REMARK 3 T11: 0.2431 T22: 0.2668 REMARK 3 T33: 0.2487 T12: -0.0274 REMARK 3 T13: 0.0199 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 3.6051 L22: 5.6368 REMARK 3 L33: 4.6095 L12: 0.4748 REMARK 3 L13: -1.1072 L23: -2.0054 REMARK 3 S TENSOR REMARK 3 S11: -0.0788 S12: 0.3925 S13: 0.0478 REMARK 3 S21: -0.4374 S22: 0.2422 S23: 0.1137 REMARK 3 S31: 0.3452 S32: -0.3986 S33: -0.1856 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 8IJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-22 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9121 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.752 REMARK 200 RESOLUTION RANGE LOW (A) : 20.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5IMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, ZN(OAC)2, MES, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294.15K 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 12.45750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.68800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.60250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.68800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.45750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.60250 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 ASP A 2 REMARK 465 VAL A 3 REMARK 465 GLY A 27 REMARK 465 ARG A 28 REMARK 465 VAL A 62 REMARK 465 SER A 63 REMARK 465 LEU A 64 REMARK 465 GLU A 65 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 OE1 GLN A 4 O HOH A 301 2.00 REMARK 500 N GLY A 66 O HOH A 302 2.09 REMARK 500 OE1 GLU A 45 O HOH A 303 2.09 REMARK 500 OE2 GLU A 89 O HOH A 304 2.14 REMARK 500 OE2 GLU A 47 O HOH A 305 2.18 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 SER A 85 71.88 73.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 45 OE1 REMARK 620 2 GLU A 45 OE2 57.9 REMARK 620 3 ASP A 73 OD2 79.0 24.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 60 OD2 REMARK 620 2 ASP A 111 OD1 71.3 REMARK 620 3 ASP A 111 OD2 76.1 5.4 REMARK 620 N 1 2 DBREF 8IJS A 1 126 PDB 8IJS 8IJS 1 126 SEQRES 1 A 126 MET ASP VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL SEQRES 2 A 126 ASN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 A 126 GLY ARG THR PHE SER SER TYR SER MET GLY TRP PHE ARG SEQRES 4 A 126 GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL VAL ALA ILE SEQRES 5 A 126 SER LYS GLY GLY TYR LYS TYR ASP ALA VAL SER LEU GLU SEQRES 6 A 126 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 126 VAL TYR LEU GLN ILE ASN SER LEU ARG PRO GLU ASP THR SEQRES 8 A 126 ALA VAL TYR TYR CYS ALA SER SER ARG ALA TYR GLY SER SEQRES 9 A 126 SER ARG LEU ARG LEU ALA ASP THR TYR GLU TYR TRP GLY SEQRES 10 A 126 GLN GLY THR LEU VAL THR VAL SER SER HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *41(H2 O) HELIX 1 AA1 THR A 29 TYR A 33 5 5 HELIX 2 AA2 ASN A 74 LYS A 76 5 3 HELIX 3 AA3 ARG A 87 THR A 91 5 5 HELIX 4 AA4 SER A 104 TYR A 113 5 10 SHEET 1 AA1 4 LEU A 5 SER A 8 0 SHEET 2 AA1 4 SER A 18 ALA A 25 -1 O ALA A 24 N VAL A 6 SHEET 3 AA1 4 THR A 78 ASN A 84 -1 O LEU A 81 N LEU A 21 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 6 LEU A 12 VAL A 13 0 SHEET 2 AA2 6 THR A 120 VAL A 124 1 O THR A 123 N VAL A 13 SHEET 3 AA2 6 ALA A 92 SER A 99 -1 N TYR A 94 O THR A 120 SHEET 4 AA2 6 SER A 34 GLN A 40 -1 N PHE A 38 O TYR A 95 SHEET 5 AA2 6 GLU A 47 ILE A 52 -1 O ILE A 52 N MET A 35 SHEET 6 AA2 6 LYS A 58 ASP A 60 -1 O TYR A 59 N ALA A 51 SHEET 1 AA3 4 LEU A 12 VAL A 13 0 SHEET 2 AA3 4 THR A 120 VAL A 124 1 O THR A 123 N VAL A 13 SHEET 3 AA3 4 ALA A 92 SER A 99 -1 N TYR A 94 O THR A 120 SHEET 4 AA3 4 TYR A 115 TRP A 116 -1 O TYR A 115 N SER A 98 SSBOND 1 CYS A 23 CYS A 96 1555 1555 2.02 LINK OE1 GLU A 45 ZN ZN A 202 1555 3554 2.26 LINK OE2 GLU A 45 ZN ZN A 202 1555 3554 2.29 LINK OD2 ASP A 60 ZN ZN A 201 1555 1555 1.90 LINK OD2 ASP A 73 ZN ZN A 202 1555 1555 2.25 LINK OD1 ASP A 111 ZN ZN A 201 1555 1455 2.41 LINK OD2 ASP A 111 ZN ZN A 201 1555 1455 2.38 CRYST1 24.915 53.205 65.376 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 0.040136 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015296 0.00000