HEADER LIPID TRANSPORT 14-FEB-18 6CFE TITLE CRYSTAL STRUCTURE OF C2S5: A COMPUTATIONALLY DESIGNED IMMUNOGEN TO TITLE 2 TARGET CARBOHYDRATE-OCCLUDED EPITOPES ON THE HIV ENVELOPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTANT OF APOLIPOPROTEIN E3 (APO-E3); 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; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS IMMUNOGEN, HIV-1, GP120, PROTEIN DESIGN, MUTANT OF APOLIPOPROTEIN E3 KEYWDS 2 (APO-E3), LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.ZHU,H.M.KE,R.SWANSTROM,N.V.DOKHOLYAN REVDAT 5 04-OCT-23 6CFE 1 REMARK REVDAT 4 18-DEC-19 6CFE 1 REMARK REVDAT 3 13-MAR-19 6CFE 1 JRNL REVDAT 2 20-FEB-19 6CFE 1 REMARK REVDAT 1 06-FEB-19 6CFE 0 JRNL AUTH C.ZHU,E.DUKHOVLINOVA,O.COUNCIL,L.PING,E.M.FAISON,S.S.PRABHU, JRNL AUTH 2 E.L.POTTER,S.L.UPTON,G.YIN,J.M.FAY,L.P.KINCER,E.SPIELVOGEL, JRNL AUTH 3 S.L.CAMPBELL,S.R.BENHABBOUR,H.KE,R.SWANSTROM,N.V.DOKHOLYAN JRNL TITL RATIONALLY DESIGNED CARBOHYDRATE-OCCLUDED EPITOPES ELICIT JRNL TITL 2 HIV-1 ENV-SPECIFIC ANTIBODIES. JRNL REF NAT COMMUN V. 10 948 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30814513 JRNL DOI 10.1038/S41467-019-08876-W REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 637 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 39.0115 - 3.4091 1.00 2583 139 0.2013 0.2127 REMARK 3 2 3.4091 - 2.7061 1.00 2440 127 0.2762 0.3525 REMARK 3 3 2.7061 - 2.3641 1.00 2412 126 0.2752 0.2992 REMARK 3 4 2.3641 - 2.1480 1.00 2393 124 0.2671 0.3257 REMARK 3 5 2.1480 - 1.9940 0.99 2384 121 0.2942 0.3709 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.17 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 : 0.004 1170 REMARK 3 ANGLE : 0.513 1572 REMARK 3 CHIRALITY : 0.028 175 REMARK 3 PLANARITY : 0.002 205 REMARK 3 DIHEDRAL : 13.967 731 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 23:80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.947 -12.439 -10.428 REMARK 3 T TENSOR REMARK 3 T11: 0.4114 T22: 0.3960 REMARK 3 T33: 0.3611 T12: 0.0249 REMARK 3 T13: 0.0589 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 3.2752 L22: 2.5758 REMARK 3 L33: 3.1995 L12: 0.2495 REMARK 3 L13: 0.3783 L23: 1.7006 REMARK 3 S TENSOR REMARK 3 S11: -0.0779 S12: 0.5157 S13: -0.1674 REMARK 3 S21: -0.3963 S22: 0.1567 S23: -0.1444 REMARK 3 S31: -0.4870 S32: -0.0383 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 81:123 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.263 -9.678 -9.634 REMARK 3 T TENSOR REMARK 3 T11: 0.5913 T22: 0.6865 REMARK 3 T33: 0.5327 T12: 0.1397 REMARK 3 T13: -0.0143 T23: -0.0820 REMARK 3 L TENSOR REMARK 3 L11: 1.7249 L22: 0.0937 REMARK 3 L33: 0.9656 L12: 0.1042 REMARK 3 L13: -0.2167 L23: -0.2518 REMARK 3 S TENSOR REMARK 3 S11: -0.1854 S12: 0.1872 S13: 0.6038 REMARK 3 S21: -0.0472 S22: -0.1298 S23: 0.5705 REMARK 3 S31: -0.1156 S32: -0.5991 S33: -0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 124:159 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.487 -9.742 0.855 REMARK 3 T TENSOR REMARK 3 T11: 0.3633 T22: 0.5302 REMARK 3 T33: 0.4597 T12: 0.0550 REMARK 3 T13: 0.0572 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.9590 L22: 0.6088 REMARK 3 L33: 2.7300 L12: -0.3639 REMARK 3 L13: -0.5099 L23: 0.9318 REMARK 3 S TENSOR REMARK 3 S11: 0.4067 S12: -0.2124 S13: 0.4886 REMARK 3 S21: 0.3375 S22: -0.5639 S23: 0.4154 REMARK 3 S31: 0.3767 S32: -0.7813 S33: 0.0032 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 6CFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232649. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-16 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 18.00 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 16.50 REMARK 200 R MERGE FOR SHELL (I) : 0.88600 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: PHENIX REMARK 200 STARTING MODEL: 1BZ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 20000, 100 MM MES PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 46.80567 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 93.61133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 93.61133 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 46.80567 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 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 GLY A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLU A 11 REMARK 465 ASN A 12 REMARK 465 LEU A 13 REMARK 465 TYR A 14 REMARK 465 PHE A 15 REMARK 465 GLN A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 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 HH22 ARG A 99 OD2 ASP A 150 1.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 6CFE A 1 159 PDB 6CFE 6CFE 1 159 SEQRES 1 A 159 MET GLY HIS HIS HIS HIS HIS HIS GLY SER GLU ASN LEU SEQRES 2 A 159 TYR PHE GLN GLY SER GLY GLN ARG TRP GLU LEU ALA LEU SEQRES 3 A 159 GLY ARG PHE TRP ASP TYR LEU ARG TRP VAL GLN THR LEU SEQRES 4 A 159 SER GLU GLN VAL GLN GLU GLU LEU LEU SER SER GLN VAL SEQRES 5 A 159 GLU THR LYS LEU ASN LYS LEU MET GLN ARG THR MET GLU SEQRES 6 A 159 GLU LEU LYS ALA TYR LYS SER GLU LEU GLU GLU GLN LEU SEQRES 7 A 159 THR PRO VAL ALA GLU GLU THR ARG ALA ARG LEU SER LYS SEQRES 8 A 159 GLU LEU GLN ALA ALA GLN ALA ARG LEU GLY ALA ASP MET SEQRES 9 A 159 GLU ASP VAL CYS GLY ARG LEU VAL GLN TYR ARG GLY GLU SEQRES 10 A 159 VAL GLN ALA MET LEU GLY GLN SER THR GLU GLU LEU ARG SEQRES 11 A 159 VAL ARG LEU ALA THR HIS LEU ASN LYS LEU ARG GLN ARG SEQRES 12 A 159 LEU LEU GLU ASP ALA ASP ASP LEU GLN LYS ARG LEU ALA SEQRES 13 A 159 VAL TYR GLN FORMUL 2 HOH *17(H2 O) HELIX 1 AA1 GLN A 20 LEU A 39 1 20 HELIX 2 AA2 SER A 40 SER A 49 1 10 HELIX 3 AA3 SER A 50 LEU A 78 1 29 HELIX 4 AA4 ALA A 82 ALA A 120 1 39 HELIX 5 AA5 THR A 126 GLN A 159 1 34 CRYST1 46.883 46.883 140.417 90.00 90.00 120.00 P 31 2 1 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 0.021330 0.012315 0.000000 0.00000 SCALE2 0.000000 0.024629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007122 0.00000