HEADER T-CELL SURFACE GLYCOPROTEIN 11-NOV-96 1CDY TITLE STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4 MUTANT WITH GLY 47 TITLE 2 REPLACED BY SER COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: D1D2 FRAGMENT; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: OVARY; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS IMMUNOGLOBULIN FOLD, TRANSMEMBRANE, GLYCOPROTEIN, T-CELL, MHC, KEYWDS 2 LIPOPROTEIN, T-CELL SURFACE GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WU,D.MYSZKA,S.W.TENDIAN,C.G.BROUILLETTE,R.W.SWEET,I.M.CHAIKEN, AUTHOR 2 W.A.HENDRICKSON REVDAT 3 16-NOV-11 1CDY 1 VERSN HETATM REVDAT 2 24-FEB-09 1CDY 1 VERSN REVDAT 1 01-APR-97 1CDY 0 JRNL AUTH H.WU,D.G.MYSZKA,S.W.TENDIAN,C.G.BROUILLETTE,R.W.SWEET, JRNL AUTH 2 I.M.CHAIKEN,W.A.HENDRICKSON JRNL TITL KINETIC AND STRUCTURAL ANALYSIS OF MUTANT CD4 RECEPTORS THAT JRNL TITL 2 ARE DEFECTIVE IN HIV GP120 BINDING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 93 15030 1996 JRNL REFN ISSN 0027-8424 JRNL PMID 8986758 JRNL DOI 10.1073/PNAS.93.26.15030 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 10876 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1385 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 207 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 2.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CDY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.10000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.10000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.95000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 261 LIES ON A SPECIAL POSITION. 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 CB VAL A 12 O HOH A 354 1.97 REMARK 500 O HOH A 257 O HOH A 395 2.02 REMARK 500 OE1 GLN A 112 O HOH A 387 2.07 REMARK 500 NZ LYS A 142 O HOH A 332 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 37 CA - CB - CG ANGL. DEV. = 20.1 DEGREES REMARK 500 LEU A 74 CA - CB - CG ANGL. DEV. = 14.8 DEGREES 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 19 -54.21 -142.41 REMARK 500 GLN A 20 171.79 -58.80 REMARK 500 LYS A 21 131.33 -31.84 REMARK 500 SER A 23 119.43 52.32 REMARK 500 ILE A 24 -146.42 -153.07 REMARK 500 GLN A 33 30.39 37.55 REMARK 500 LYS A 50 2.18 -69.41 REMARK 500 ASP A 80 177.53 178.87 REMARK 500 GLU A 87 -117.62 46.86 REMARK 500 SER A 104 65.14 -66.82 REMARK 500 ASP A 105 -24.72 48.59 REMARK 500 THR A 106 -14.50 67.74 REMARK 500 PRO A 126 -149.53 -119.36 REMARK 500 PRO A 133 -4.34 -59.23 REMARK 500 GLN A 152 -7.07 -58.35 REMARK 500 GLN A 163 116.41 -171.11 REMARK 500 GLN A 165 -27.16 67.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 288 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 294 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH A 319 DISTANCE = 5.56 ANGSTROMS REMARK 525 HOH A 321 DISTANCE = 20.54 ANGSTROMS REMARK 525 HOH A 325 DISTANCE = 22.92 ANGSTROMS REMARK 525 HOH A 340 DISTANCE = 13.66 ANGSTROMS REMARK 525 HOH A 348 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH A 381 DISTANCE = 21.91 ANGSTROMS REMARK 525 HOH A 392 DISTANCE = 5.56 ANGSTROMS REMARK 525 HOH A 403 DISTANCE = 16.47 ANGSTROMS REMARK 525 HOH A 404 DISTANCE = 5.82 ANGSTROMS DBREF 1CDY A 1 178 UNP P01730 CD4_HUMAN 26 203 SEQADV 1CDY SER A 47 UNP P01730 GLY 72 ENGINEERED SEQRES 1 A 178 LYS LYS VAL VAL LEU GLY LYS LYS GLY ASP THR VAL GLU SEQRES 2 A 178 LEU THR CYS THR ALA SER GLN LYS LYS SER ILE GLN PHE SEQRES 3 A 178 HIS TRP LYS ASN SER ASN GLN ILE LYS ILE LEU GLY ASN SEQRES 4 A 178 GLN GLY SER PHE LEU THR LYS SER PRO SER LYS LEU ASN SEQRES 5 A 178 ASP ARG ALA ASP SER ARG ARG SER LEU TRP ASP GLN GLY SEQRES 6 A 178 ASN PHE PRO LEU ILE ILE LYS ASN LEU LYS ILE GLU ASP SEQRES 7 A 178 SER ASP THR TYR ILE CYS GLU VAL GLU ASP GLN LYS GLU SEQRES 8 A 178 GLU VAL GLN LEU LEU VAL PHE GLY LEU THR ALA ASN SER SEQRES 9 A 178 ASP THR HIS LEU LEU GLN GLY GLN SER LEU THR LEU THR SEQRES 10 A 178 LEU GLU SER PRO PRO GLY SER SER PRO SER VAL GLN CYS SEQRES 11 A 178 ARG SER PRO ARG GLY LYS ASN ILE GLN GLY GLY LYS THR SEQRES 12 A 178 LEU SER VAL SER GLN LEU GLU LEU GLN ASP SER GLY THR SEQRES 13 A 178 TRP THR CYS THR VAL LEU GLN ASN GLN LYS LYS VAL GLU SEQRES 14 A 178 PHE LYS ILE ASP ILE VAL VAL LEU ALA FORMUL 2 HOH *207(H2 O) HELIX 1 1 ASN A 52 ARG A 54 5 3 HELIX 2 2 ARG A 59 GLN A 64 1 6 HELIX 3 3 ILE A 76 ASP A 78 5 3 SHEET 1 D1A 3 ARG A 54 ARG A 58 0 SHEET 2 D1A 3 GLN A 64 LYS A 72 -1 SHEET 3 D1A 3 VAL A 12 ALA A 18 -1 SHEET 1 D1B 6 LYS A 2 LYS A 8 0 SHEET 2 D1B 6 GLN A 89 PHE A 98 1 SHEET 3 D1B 6 ASP A 80 VAL A 86 -1 SHEET 4 D1B 6 GLN A 25 SER A 31 -1 SHEET 5 D1B 6 ILE A 34 GLN A 40 -1 SHEET 6 D1B 6 PHE A 43 SER A 47 -1 SHEET 1 D2A 3 LYS A 142 LEU A 149 0 SHEET 2 D2A 3 GLY A 111 GLU A 119 -1 SHEET 3 D2A 3 GLY A 99 ASN A 103 -1 SHEET 1 D2B 4 LYS A 166 ILE A 174 0 SHEET 2 D2B 4 GLY A 155 GLN A 163 -1 SHEET 3 D2B 4 SER A 127 SER A 132 -1 SHEET 4 D2B 4 LYS A 136 GLY A 140 -1 SSBOND 1 CYS A 16 CYS A 84 1555 1555 1.98 SSBOND 2 CYS A 130 CYS A 159 1555 1555 2.03 CRYST1 82.200 29.900 85.500 90.00 115.30 90.00 C 1 2 1 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 0.012165 0.000000 0.005751 0.00000 SCALE2 0.000000 0.033445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012937 0.00000 MASTER 295 0 0 3 16 0 0 6 0 0 0 14 END