PDB Short entry for 1YDP HEADER IMMUNE SYSTEM 25-DEC-04 1YDP TITLE 1.9A CRYSTAL STRUCTURE OF HLA-G COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS I ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HLA-G HEAVY CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: HLA-G, HDCMA22P; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: HISTONE 2A PEPTIDE; COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.S.CLEMENTS,L.KJER-NIELSEN,L.KOSTENKO,H.L.HOARE,M.A.DUNSTONE, AUTHOR 2 E.MOSES,K.FREED,A.G.BROOKS,J.ROSSJOHN,J.MCCLUSKEY REVDAT 4 10-NOV-21 1YDP 1 REMARK SEQADV LINK REVDAT 3 25-JUL-18 1YDP 1 COMPND SOURCE REVDAT 2 24-FEB-09 1YDP 1 VERSN REVDAT 1 08-MAR-05 1YDP 0 JRNL AUTH C.S.CLEMENTS,L.KJER-NIELSEN,L.KOSTENKO,H.L.HOARE, JRNL AUTH 2 M.A.DUNSTONE,E.MOSES,K.FREED,A.G.BROOKS,J.ROSSJOHN, JRNL AUTH 3 J.MCCLUSKEY JRNL TITL CRYSTAL STRUCTURE OF HLA-G: A NONCLASSICAL MHC CLASS I JRNL TITL 2 MOLECULE EXPRESSED AT THE FETAL-MATERNAL INTERFACE JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 3360 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15718280 JRNL DOI 10.1073/PNAS.0409676102 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 40820 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) : 0.235 REMARK 3 FREE R VALUE : 0.264 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 : 3160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 427 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1YDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031411. 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) : M 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 : 130133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 101.14667 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 50.57333 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 50.57333 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 101.14667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 APPLY THE FOLLOWING TO CHAINS: A, P REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 38.57500 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 66.81386 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 101.14667 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 538 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 O VAL B 9 N TYR B 10 1.59 REMARK 500 CD ARG A 108 O HOH A 385 1.93 REMARK 500 OD2 ASP A 102 NE ARG A 111 1.98 REMARK 500 NE ARG A 111 O HOH A 462 2.11 REMARK 500 NH1 ARG A 6 CE1 TYR A 113 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CZ PHE A 195 O HOH A 568 5565 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 176 C GLU A 177 N -0.200 REMARK 500 ALA A 182 C ASP A 183 N 0.284 REMARK 500 THR A 190 C HIS A 191 N -0.204 REMARK 500 TRP A 217 C GLN A 218 N 0.223 REMARK 500 ARG A 219 CA ARG A 219 CB -0.151 REMARK 500 LEU A 266 CB LEU A 266 CG 0.305 REMARK 500 PRO A 267 CB PRO A 267 CG 0.409 REMARK 500 PRO A 267 CD PRO A 267 N 0.156 REMARK 500 GLU A 268 CB GLU A 268 CG -0.307 REMARK 500 GLU A 268 C PRO A 269 N -0.133 REMARK 500 VAL B 9 C TYR B 10 N -0.368 REMARK 500 ARG B 12 CD ARG B 12 NE -0.286 REMARK 500 ALA B 15 C GLU B 16 N 0.313 REMARK 500 GLU B 16 C ASN B 17 N -0.260 REMARK 500 ASN B 17 CB ASN B 17 CG -0.184 REMARK 500 VAL B 82 C ASN B 83 N 0.256 REMARK 500 ASN B 83 C HIS B 84 N -0.221 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 ARG A 6 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 GLN A 79 C - N - CA ANGL. DEV. = -17.1 DEGREES REMARK 500 TYR A 113 CB - CA - C ANGL. DEV. = -14.8 DEGREES REMARK 500 TYR A 113 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LYS A 176 CA - C - N ANGL. DEV. = 16.4 DEGREES REMARK 500 LYS A 176 O - C - N ANGL. DEV. = -16.4 DEGREES REMARK 500 ASP A 183 C - N - CA ANGL. DEV. = -17.1 DEGREES REMARK 500 THR A 190 CA - C - N ANGL. DEV. = 13.8 DEGREES REMARK 500 THR A 190 O - C - N ANGL. DEV. = -13.6 DEGREES REMARK 500 PHE A 195 C - N - CA ANGL. DEV. = -22.1 DEGREES REMARK 500 PHE A 195 CA - CB - CG ANGL. DEV. = 16.5 DEGREES REMARK 500 PHE A 195 CB - CG - CD2 ANGL. DEV. = 10.1 DEGREES REMARK 500 PHE A 195 CB - CG - CD1 ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG A 219 CB - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG A 219 CD - NE - CZ ANGL. DEV. = 40.1 DEGREES REMARK 500 ASP A 220 CA - CB - CG ANGL. DEV. = 20.1 DEGREES REMARK 500 ASP A 220 CB - CG - OD1 ANGL. DEV. = -18.8 DEGREES REMARK 500 ASP A 220 CB - CG - OD2 ANGL. DEV. = 19.2 DEGREES REMARK 500 LEU A 266 CB - CG - CD1 ANGL. DEV. = 18.5 DEGREES REMARK 500 PRO A 267 N - CA - CB ANGL. DEV. = 7.6 DEGREES REMARK 500 PRO A 267 CA - CB - CG ANGL. DEV. = -11.4 DEGREES REMARK 500 GLU A 268 CA - CB - CG ANGL. DEV. = 23.1 DEGREES REMARK 500 VAL B 9 CA - C - N ANGL. DEV. = 29.9 DEGREES REMARK 500 VAL B 9 O - C - N ANGL. DEV. = -30.8 DEGREES REMARK 500 GLU B 16 C - N - CA ANGL. DEV. = -18.7 DEGREES REMARK 500 ASN B 83 C - N - CA ANGL. DEV. = -17.1 DEGREES REMARK 500 ASN B 83 CA - C - N ANGL. DEV. = 13.7 DEGREES REMARK 500 ASN B 83 O - C - N ANGL. DEV. = -12.1 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 ARG A 14 70.58 -153.50 REMARK 500 ASP A 29 -129.17 59.02 REMARK 500 TRP A 51 1.09 -66.95 REMARK 500 GLU A 114 118.18 163.85 REMARK 500 TYR A 123 -62.54 -120.46 REMARK 500 GLN A 180 44.11 -98.62 REMARK 500 PHE A 195 -88.34 -54.14 REMARK 500 THR A 225 -48.09 -15.82 REMARK 500 LYS A 243 143.96 -173.04 REMARK 500 TRP B 60 -13.73 82.19 REMARK 500 THR B 68 145.50 -177.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 194 PHE A 195 -147.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 219 0.08 SIDE CHAIN REMARK 500 ARG B 12 0.22 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 183 -13.80 REMARK 500 GLU A 268 16.04 REMARK 500 VAL B 9 19.61 REMARK 500 ALA B 15 10.19 REMARK 500 GLU B 16 -19.89 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 CO B1001 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 169 ND1 REMARK 620 2 ASP A 196 OD2 99.8 REMARK 620 3 MET B 1A N 174.6 82.8 REMARK 620 4 MET B 1A O 100.6 148.2 79.1 REMARK 620 5 CL B1002 CL 91.2 112.9 83.4 90.9 REMARK 620 6 CL B1003 CL 96.6 63.9 88.8 89.6 171.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1003 DBREF 1YDP A 2 276 UNP P17693 HLAG_HUMAN 26 300 DBREF 1YDP B 1B 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1YDP P 1 9 PDB 1YDP 1YDP 1 9 SEQADV 1YDP SER A 42 UNP P17693 CYS 66 ENGINEERED MUTATION SEQADV 1YDP MET B 1A UNP P61769 INITIATING METHIONINE SEQRES 1 A 275 SER HIS SER MET ARG TYR PHE SER ALA ALA VAL SER ARG SEQRES 2 A 275 PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA MET GLY TYR SEQRES 3 A 275 VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SER SEQRES 4 A 275 ALA SER PRO ARG MET GLU PRO ARG ALA PRO TRP VAL GLU SEQRES 5 A 275 GLN GLU GLY PRO GLU TYR TRP GLU GLU GLU THR ARG ASN SEQRES 6 A 275 THR LYS ALA HIS ALA GLN THR ASP ARG MET ASN LEU GLN SEQRES 7 A 275 THR LEU ARG GLY TYR TYR ASN GLN SER GLU ALA SER SER SEQRES 8 A 275 HIS THR LEU GLN TRP MET ILE GLY CYS ASP LEU GLY SER SEQRES 9 A 275 ASP GLY ARG LEU ILE ARG GLY TYR GLU ARG TYR ALA TYR SEQRES 10 A 275 ASP GLY LYS ASP TYR LEU ALA LEU ASN GLU ASP LEU ARG SEQRES 11 A 275 SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE SER LYS SEQRES 12 A 275 ARG LYS CYS GLU ALA ALA ASN VAL ALA GLU GLN ARG ARG SEQRES 13 A 275 ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU HIS ARG SEQRES 14 A 275 TYR LEU GLU ASN GLY LYS GLU MET LEU GLN ARG ALA ASP SEQRES 15 A 275 PRO PRO LYS THR HIS VAL THR HIS HIS PRO VAL PHE ASP SEQRES 16 A 275 TYR GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE TYR SEQRES 17 A 275 PRO ALA GLU ILE ILE LEU THR TRP GLN ARG ASP GLY GLU SEQRES 18 A 275 ASP GLN THR GLN ASP VAL GLU LEU VAL GLU THR ARG PRO SEQRES 19 A 275 ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA VAL VAL SEQRES 20 A 275 VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS VAL SEQRES 21 A 275 GLN HIS GLU GLY LEU PRO GLU PRO LEU MET LEU ARG TRP SEQRES 22 A 275 LYS GLN SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 P 9 ARG ILE ILE PRO ARG HIS LEU GLN LEU HET CO B1001 1 HET CL B1002 1 HET CL B1003 1 HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE ION FORMUL 4 CO CO 2+ FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *427(H2 O) HELIX 1 1 ALA A 49 GLU A 53 5 5 HELIX 2 2 GLY A 56 TYR A 85 1 30 HELIX 3 3 ASP A 137 ASN A 151 1 15 HELIX 4 4 VAL A 152 GLY A 162 1 11 HELIX 5 5 GLY A 162 GLY A 175 1 14 HELIX 6 6 GLY A 175 GLN A 180 1 6 HELIX 7 7 GLN A 224 VAL A 228 5 5 HELIX 8 8 GLU A 253 GLN A 255 5 3 SHEET 1 A 8 GLU A 46 PRO A 47 0 SHEET 2 A 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 A 8 ARG A 21 VAL A 28 -1 N ALA A 24 O PHE A 36 SHEET 4 A 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 A 8 THR A 94 LEU A 103 -1 O LEU A 103 N HIS A 3 SHEET 6 A 8 LEU A 109 TYR A 118 -1 O ALA A 117 N GLN A 96 SHEET 7 A 8 LYS A 121 LEU A 126 -1 O LEU A 124 N TYR A 116 SHEET 8 A 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 B 4 LYS A 186 HIS A 192 0 SHEET 2 B 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 B 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 B 4 GLU A 229 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 C 4 LYS A 186 HIS A 192 0 SHEET 2 C 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 C 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 C 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 D 3 ILE A 214 ARG A 219 0 SHEET 2 D 3 TYR A 257 GLN A 262 -1 O THR A 258 N GLN A 218 SHEET 3 D 3 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 E 4 LYS B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 E 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 E 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 F 4 LYS B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 F 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 F 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 G 4 GLU B 44 ARG B 45 0 SHEET 2 G 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 G 4 TYR B 78 ASN B 83 -1 O ARG B 81 N ASP B 38 SHEET 4 G 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.05 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.03 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.03 LINK ND1 HIS A 169 CO CO B1001 6665 1555 2.23 LINK OD2 ASP A 196 CO CO B1001 3565 1555 2.70 LINK N MET B 1A CO CO B1001 1555 1555 2.18 LINK O MET B 1A CO CO B1001 1555 1555 2.14 LINK CO CO B1001 CL CL B1002 1555 1555 2.25 LINK CO CO B1001 CL CL B1003 1555 1555 2.21 CISPEP 1 TYR A 209 PRO A 210 0 -0.27 CISPEP 2 HIS B 31 PRO B 32 0 -0.15 SITE 1 AC1 5 HIS A 169 ASP A 196 MET B 1A CL B1002 SITE 2 AC1 5 CL B1003 SITE 1 AC2 5 HIS A 169 MET B 1A GLN B 2 CO B1001 SITE 2 AC2 5 HOH B1060 SITE 1 AC3 6 HIS A 169 LEU A 172 ASP A 196 HOH A 552 SITE 2 AC3 6 MET B 1A CO B1001 CRYST1 77.150 77.150 151.720 90.00 90.00 120.00 P 32 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 0.012962 0.007483 -0.000001 0.00000 SCALE2 0.000000 0.014967 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.006591 0.00000