HEADER CYTOSOLIC PROTEIN 11-MAY-23 8P0Z TITLE AP01-S2.3 - A VARIANT OF A REDESIGNED TRANSFERRIN RECEPTOR APICAL TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFERRIN RECEPTOR PROTEIN 1, SERUM FORM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STFR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TFRC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21* (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS RECEPTOR DOMAIN, TRANSFERRIN, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.OBERDORFER,B.GRILL,S.BJELIC,D.STOLL REVDAT 1 27-SEP-23 8P0Z 0 JRNL AUTH D.J.SJOSTROM,B.GRILL,E.AMBROSETTI,A.A.VEETIL,C.MOHLIN, JRNL AUTH 2 A.I.TEIXEIRA,G.OBERDOFER,S.BJELIC JRNL TITL AFFINITY MATURATED TRANSFERRIN RECEPTOR APICAL DOMAIN BLOCKS JRNL TITL 2 MACHUPO VIRUS GLYCOPROTEIN BINDING. JRNL REF J.MOL.BIOL. V. 435 68262 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 37678707 JRNL DOI 10.1016/J.JMB.2023.168262 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC1_3777 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 10664 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 535 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 35.9500 - 2.9800 0.98 2588 137 0.1787 0.2067 REMARK 3 2 2.9800 - 2.3700 0.97 2534 133 0.2282 0.2410 REMARK 3 3 2.3700 - 2.0700 0.97 2511 133 0.2543 0.2840 REMARK 3 4 2.0700 - 1.8800 0.96 2497 132 0.3280 0.3286 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) : 0.255 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.304 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.35 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 : 0.003 1290 REMARK 3 ANGLE : 0.647 1751 REMARK 3 CHIRALITY : 0.050 203 REMARK 3 PLANARITY : 0.003 229 REMARK 3 DIHEDRAL : 13.446 484 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 8P0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292129913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-22 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 : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 35.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.19200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.18900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.750 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11 MG/ML PROTEIN IN 20 MM HEPES, PH REMARK 280 6.8, 150 MM NACL MIXED WITH 100 MM MIB BUFFER, PH 7.5, AND 24 % REMARK 280 PEG IN A RATIO 1:2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.68500 REMARK 290 SMTRY3 2 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 ARG A 158 REMARK 465 GLY A 159 REMARK 465 SER A 160 REMARK 465 LEU A 161 REMARK 465 GLU A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 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 GLN A 2 85.28 20.39 REMARK 500 ASN A 41 -114.20 54.94 REMARK 500 LYS A 66 -46.61 72.95 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 145 OG1 REMARK 620 2 SER A 146 O 85.3 REMARK 620 3 LYS A 149 O 74.2 60.7 REMARK 620 N 1 2 DBREF 8P0Z A 2 104 UNP P02786 TFR1_HUMAN 197 299 DBREF 8P0Z A 110 155 UNP P02786 TFR1_HUMAN 332 377 SEQADV 8P0Z MET A 1 UNP P02786 INITIATING METHIONINE SEQADV 8P0Z GLU A 15 UNP P02786 VAL 210 CONFLICT SEQADV 8P0Z SER A 24 UNP P02786 TYR 219 CONFLICT SEQADV 8P0Z ASN A 27 UNP P02786 TYR 222 CONFLICT SEQADV 8P0Z THR A 103 UNP P02786 PHE 298 CONFLICT SEQADV 8P0Z LYS A 105 UNP P02786 LINKER SEQADV 8P0Z GLY A 106 UNP P02786 LINKER SEQADV 8P0Z LYS A 107 UNP P02786 LINKER SEQADV 8P0Z SER A 108 UNP P02786 LINKER SEQADV 8P0Z GLY A 109 UNP P02786 LINKER SEQADV 8P0Z GLU A 118 UNP P02786 ALA 340 CONFLICT SEQADV 8P0Z GLY A 156 UNP P02786 EXPRESSION TAG SEQADV 8P0Z GLY A 157 UNP P02786 EXPRESSION TAG SEQADV 8P0Z ARG A 158 UNP P02786 EXPRESSION TAG SEQADV 8P0Z GLY A 159 UNP P02786 EXPRESSION TAG SEQADV 8P0Z SER A 160 UNP P02786 EXPRESSION TAG SEQADV 8P0Z LEU A 161 UNP P02786 EXPRESSION TAG SEQADV 8P0Z GLU A 162 UNP P02786 EXPRESSION TAG SEQADV 8P0Z HIS A 163 UNP P02786 EXPRESSION TAG SEQADV 8P0Z HIS A 164 UNP P02786 EXPRESSION TAG SEQADV 8P0Z HIS A 165 UNP P02786 EXPRESSION TAG SEQADV 8P0Z HIS A 166 UNP P02786 EXPRESSION TAG SEQADV 8P0Z HIS A 167 UNP P02786 EXPRESSION TAG SEQADV 8P0Z HIS A 168 UNP P02786 EXPRESSION TAG SEQRES 1 A 168 MET GLN ASN SER VAL ILE ILE VAL ASP LYS ASN GLY ARG SEQRES 2 A 168 LEU GLU TYR LEU VAL GLU ASN PRO GLY GLY SER VAL ALA SEQRES 3 A 168 ASN SER LYS ALA ALA THR VAL THR GLY LYS LEU VAL HIS SEQRES 4 A 168 ALA ASN PHE GLY THR LYS LYS ASP PHE GLU ASP LEU TYR SEQRES 5 A 168 THR PRO VAL ASN GLY SER ILE VAL ILE VAL ARG ALA GLY SEQRES 6 A 168 LYS ILE THR PHE ALA GLU LYS VAL ALA ASN ALA GLU SER SEQRES 7 A 168 LEU ASN ALA ILE GLY VAL LEU ILE TYR MET ASP GLN THR SEQRES 8 A 168 LYS PHE PRO ILE VAL ASN ALA GLU LEU SER PHE THR GLY SEQRES 9 A 168 LYS GLY LYS SER GLY ILE PRO VAL GLN THR ILE SER ARG SEQRES 10 A 168 GLU ALA ALA GLU LYS LEU PHE GLY ASN MET GLU GLY ASP SEQRES 11 A 168 CYS PRO SER ASP TRP LYS THR ASP SER THR CYS ARG MET SEQRES 12 A 168 VAL THR SER GLU SER LYS ASN VAL LYS LEU THR VAL GLY SEQRES 13 A 168 GLY ARG GLY SER LEU GLU HIS HIS HIS HIS HIS HIS HET NA A 201 1 HET NA A 202 1 HET BO3 A 203 4 HETNAM NA SODIUM ION HETNAM BO3 BORIC ACID FORMUL 2 NA 2(NA 1+) FORMUL 4 BO3 B H3 O3 FORMUL 5 HOH *108(H2 O) HELIX 1 AA1 THR A 44 LEU A 51 1 8 HELIX 2 AA2 THR A 68 LEU A 79 1 12 HELIX 3 AA3 SER A 116 ASN A 126 1 11 HELIX 4 AA4 PRO A 132 LYS A 136 5 5 SHEET 1 AA1 4 GLU A 15 GLU A 19 0 SHEET 2 AA1 4 SER A 4 ASP A 9 -1 N VAL A 5 O GLU A 19 SHEET 3 AA1 4 LYS A 149 VAL A 155 -1 O LYS A 152 N ILE A 6 SHEET 4 AA1 4 ALA A 31 GLY A 35 -1 N GLY A 35 O VAL A 151 SHEET 1 AA2 4 LEU A 37 HIS A 39 0 SHEET 2 AA2 4 ILE A 59 ARG A 63 1 O ILE A 59 N VAL A 38 SHEET 3 AA2 4 GLY A 83 TYR A 87 1 O LEU A 85 N VAL A 60 SHEET 4 AA2 4 VAL A 112 THR A 114 1 O GLN A 113 N VAL A 84 SHEET 1 AA3 2 MET A 127 ASP A 130 0 SHEET 2 AA3 2 ARG A 142 THR A 145 -1 O VAL A 144 N GLU A 128 SSBOND 1 CYS A 131 CYS A 141 1555 1555 2.04 LINK OE1 GLU A 71 NA NA A 201 1555 1555 2.37 LINK OG1 THR A 145 NA NA A 202 1555 1555 2.54 LINK O SER A 146 NA NA A 202 1555 1555 3.10 LINK O LYS A 149 NA NA A 202 1555 1555 3.11 CRYST1 32.990 57.370 39.100 90.00 113.15 90.00 P 1 21 1 2 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 0.030312 0.000000 0.012962 0.00000 SCALE2 0.000000 0.017431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027816 0.00000