HEADER TRANSPORT PROTEIN/IMMUNE SYSTEM 21-MAR-13 4JR9 TITLE CRYSTAL STRUCTURE OF NITRATE/NITRITE EXCHANGER NARK COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE EXTRUSION PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NITRITE FACILITATOR 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: IMMUNOGLOBULIN GAMMA-2A, HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: IMMUNOGLOBULIN KAPPA, LIGHT CHAIN; COMPND 11 CHAIN: L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B1223, JW1214, NARK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 CELL: HYBRIDOMA; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 17 ORGANISM_TAXID: 10090; SOURCE 18 CELL: HYBRIDOMA KEYWDS TRANSPORTER, IMMUNOGLOBULIN, MAJOR FACILITATOR SUPERFAMILY, KEYWDS 2 EXCHANGER, TRANSPORT PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHENG,G.WISEDCHAISRI,T.GONEN REVDAT 5 20-SEP-23 4JR9 1 HETSYN REVDAT 4 29-JUL-20 4JR9 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 SITE REVDAT 3 10-JUL-13 4JR9 1 JRNL REVDAT 2 22-MAY-13 4JR9 1 JRNL REVDAT 1 15-MAY-13 4JR9 0 JRNL AUTH H.ZHENG,G.WISEDCHAISRI,T.GONEN JRNL TITL CRYSTAL STRUCTURE OF A NITRATE/NITRITE EXCHANGER. JRNL REF NATURE V. 497 647 2013 JRNL REFN ISSN 0028-0836 JRNL PMID 23665960 JRNL DOI 10.1038/NATURE12139 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 45063 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2408 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3056 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6273 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.45000 REMARK 3 B22 (A**2) : -1.30000 REMARK 3 B33 (A**2) : 3.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.56000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.344 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.260 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.750 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6462 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8807 ; 1.312 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 829 ; 5.707 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;36.604 ;23.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 962 ;19.707 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;18.506 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1007 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4832 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A STRONG DENSITY ON THE SURFACE OF NARK REMARK 3 IS LIKELY FROM THE SUGAR HEAD GROUP OF THE DECYLMALTOSIDE REMARK 3 DETERGENT USED DURING PROTEIN PURIFICATION AND IS MODELLED IN REMARK 3 THE STRUCTURE AS MALTOSE. REMARK 4 REMARK 4 4JR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999973 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.89200 REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: PDB ENTRIES 3TT1, 1F8T, 3TT3, 1MRC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG400, 0.1 M CITRIC ACID PH 3.5, REMARK 280 0.1M NACL, 0.1M LI2SO4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 69.13300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.27250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.13300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.27250 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLU A 8 REMARK 465 ARG A 9 REMARK 465 ALA A 10 REMARK 465 THR A 11 REMARK 465 LEU A 191 REMARK 465 SER A 192 REMARK 465 ILE A 193 REMARK 465 PHE A 194 REMARK 465 ALA A 195 REMARK 465 VAL A 196 REMARK 465 PHE A 197 REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 465 GLN A 200 REMARK 465 GLY A 201 REMARK 465 VAL A 202 REMARK 465 LYS A 203 REMARK 465 GLN A 204 REMARK 465 PRO A 205 REMARK 465 ASP A 206 REMARK 465 GLY A 207 REMARK 465 THR A 208 REMARK 465 GLU A 209 REMARK 465 LEU A 210 REMARK 465 TYR A 211 REMARK 465 THR A 239 REMARK 465 SER A 240 REMARK 465 LYS A 241 REMARK 465 ALA A 242 REMARK 465 SER A 243 REMARK 465 ILE A 244 REMARK 465 LYS A 245 REMARK 465 GLU A 246 REMARK 465 GLN A 247 REMARK 465 LEU A 248 REMARK 465 PRO A 249 REMARK 465 VAL A 250 REMARK 465 LEU A 251 REMARK 465 LYS A 252 REMARK 465 ARG A 253 REMARK 465 GLY A 254 REMARK 465 HIS A 255 REMARK 465 ARG A 459 REMARK 465 HIS A 460 REMARK 465 SER A 461 REMARK 465 LYS A 462 REMARK 465 LYS A 463 REMARK 465 CYS H 133 REMARK 465 GLY H 134 REMARK 465 ASP H 135 REMARK 465 THR H 136 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 161 CG CD OE1 NE2 REMARK 470 VAL A 436 CG1 CG2 REMARK 470 GLN H 1 CG CD OE1 NE2 REMARK 470 ASP H 73 CG OD1 OD2 REMARK 470 ASN H 74 CG OD1 ND2 REMARK 470 VAL H 132 CG1 CG2 REMARK 470 THR H 137 OG1 CG2 REMARK 470 SER L 17 OG REMARK 470 LYS L 102 CG CD CE NZ REMARK 470 ASN L 142 CG OD1 ND2 REMARK 470 ASN L 144 CG OD1 ND2 REMARK 470 LYS L 146 CG CD CE NZ REMARK 470 SER L 152 OG REMARK 470 GLN L 155 CG CD OE1 NE2 REMARK 470 ASN L 156 CG OD1 ND2 REMARK 470 LYS L 168 CG CD CE NZ REMARK 470 LYS L 182 CG CD CE NZ REMARK 470 ASN L 189 CG OD1 ND2 REMARK 470 GLU L 194 CD OE1 OE2 REMARK 470 LYS L 198 CG CD CE NZ 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 TRP L 162 CE2 TRP L 162 CD2 0.075 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 46 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU H 83 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 LEU H 157 CA - CB - CG ANGL. DEV. = 16.7 DEGREES REMARK 500 LEU L 95 CA - CB - CG ANGL. DEV. = 15.3 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 29 -27.39 -157.86 REMARK 500 SER A 281 35.74 -80.08 REMARK 500 LYS A 282 -21.05 -145.37 REMARK 500 LEU A 291 29.12 -76.52 REMARK 500 LEU A 315 32.39 -145.94 REMARK 500 THR A 432 -159.29 -111.22 REMARK 500 SER H 99 118.60 96.06 REMARK 500 ASN H 102 -68.27 -90.33 REMARK 500 ASN L 31 -3.39 75.16 REMARK 500 THR L 51 -45.48 69.13 REMARK 500 SER L 52 -2.65 -146.06 REMARK 500 ASN L 77 72.63 -109.79 REMARK 500 ALA L 84 175.95 173.91 REMARK 500 ASN L 92 -92.68 -73.68 REMARK 500 LEU L 94 -160.28 60.31 REMARK 500 ASN L 189 -41.83 -135.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JRE RELATED DB: PDB DBREF 4JR9 A 1 463 UNP P10903 NARK_ECOLI 1 463 DBREF 4JR9 H 1 217 PDB 4JR9 4JR9 1 217 DBREF 4JR9 L 1 211 PDB 4JR9 4JR9 1 211 SEQADV 4JR9 GLY A -2 UNP P10903 EXPRESSION TAG SEQADV 4JR9 SER A -1 UNP P10903 EXPRESSION TAG SEQADV 4JR9 HIS A 0 UNP P10903 EXPRESSION TAG SEQRES 1 A 466 GLY SER HIS MET SER HIS SER SER ALA PRO GLU ARG ALA SEQRES 2 A 466 THR GLY ALA VAL ILE THR ASP TRP ARG PRO GLU ASP PRO SEQRES 3 A 466 ALA PHE TRP GLN GLN ARG GLY GLN ARG ILE ALA SER ARG SEQRES 4 A 466 ASN LEU TRP ILE SER VAL PRO CYS LEU LEU LEU ALA PHE SEQRES 5 A 466 CYS VAL TRP MET LEU PHE SER ALA VAL ALA VAL ASN LEU SEQRES 6 A 466 PRO LYS VAL GLY PHE ASN PHE THR THR ASP GLN LEU PHE SEQRES 7 A 466 MET LEU THR ALA LEU PRO SER VAL SER GLY ALA LEU LEU SEQRES 8 A 466 ARG VAL PRO TYR SER PHE MET VAL PRO ILE PHE GLY GLY SEQRES 9 A 466 ARG ARG TRP THR ALA PHE SER THR GLY ILE LEU ILE ILE SEQRES 10 A 466 PRO CYS VAL TRP LEU GLY PHE ALA VAL GLN ASP THR SER SEQRES 11 A 466 THR PRO TYR SER VAL PHE ILE ILE ILE SER LEU LEU CYS SEQRES 12 A 466 GLY PHE ALA GLY ALA ASN PHE ALA SER SER MET ALA ASN SEQRES 13 A 466 ILE SER PHE PHE PHE PRO LYS GLN LYS GLN GLY GLY ALA SEQRES 14 A 466 LEU GLY LEU ASN GLY GLY LEU GLY ASN MET GLY VAL SER SEQRES 15 A 466 VAL MET GLN LEU VAL ALA PRO LEU VAL VAL SER LEU SER SEQRES 16 A 466 ILE PHE ALA VAL PHE GLY SER GLN GLY VAL LYS GLN PRO SEQRES 17 A 466 ASP GLY THR GLU LEU TYR LEU ALA ASN ALA SER TRP ILE SEQRES 18 A 466 TRP VAL PRO PHE LEU ALA ILE PHE THR ILE ALA ALA TRP SEQRES 19 A 466 PHE GLY MET ASN ASP LEU ALA THR SER LYS ALA SER ILE SEQRES 20 A 466 LYS GLU GLN LEU PRO VAL LEU LYS ARG GLY HIS LEU TRP SEQRES 21 A 466 ILE MET SER LEU LEU TYR LEU ALA THR PHE GLY SER PHE SEQRES 22 A 466 ILE GLY PHE SER ALA GLY PHE ALA MET LEU SER LYS THR SEQRES 23 A 466 GLN PHE PRO ASP VAL GLN ILE LEU GLN TYR ALA PHE PHE SEQRES 24 A 466 GLY PRO PHE ILE GLY ALA LEU ALA ARG SER ALA GLY GLY SEQRES 25 A 466 ALA LEU SER ASP ARG LEU GLY GLY THR ARG VAL THR LEU SEQRES 26 A 466 VAL ASN PHE ILE LEU MET ALA ILE PHE SER GLY LEU LEU SEQRES 27 A 466 PHE LEU THR LEU PRO THR ASP GLY GLN GLY GLY SER PHE SEQRES 28 A 466 MET ALA PHE PHE ALA VAL PHE LEU ALA LEU PHE LEU THR SEQRES 29 A 466 ALA GLY LEU GLY SER GLY SER THR PHE GLN MET ILE SER SEQRES 30 A 466 VAL ILE PHE ARG LYS LEU THR MET ASP ARG VAL LYS ALA SEQRES 31 A 466 GLU GLY GLY SER ASP GLU ARG ALA MET ARG GLU ALA ALA SEQRES 32 A 466 THR ASP THR ALA ALA ALA LEU GLY PHE ILE SER ALA ILE SEQRES 33 A 466 GLY ALA ILE GLY GLY PHE PHE ILE PRO LYS ALA PHE GLY SEQRES 34 A 466 SER SER LEU ALA LEU THR GLY SER PRO VAL GLY ALA MET SEQRES 35 A 466 LYS VAL PHE LEU ILE PHE TYR ILE ALA CYS VAL VAL ILE SEQRES 36 A 466 THR TRP ALA VAL TYR GLY ARG HIS SER LYS LYS SEQRES 1 H 217 GLN ILE GLN LEU VAL GLN SER GLY PRO GLY LEU LYS LYS SEQRES 2 H 217 PRO GLY GLN THR VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 H 217 TYR SER PHE THR ASP TYR GLY MET ASN TRP VAL LYS GLN SEQRES 4 H 217 ALA PRO GLY LYS GLY LEU GLU TRP MET GLY TRP ILE ASN SEQRES 5 H 217 THR SER ASN GLY TYR THR THR TYR GLY ALA ALA PHE LYS SEQRES 6 H 217 GLY ARG PHE SER PHE SER VAL ASP ASN SER ALA SER THR SEQRES 7 H 217 ALA TYR LEU GLN LEU SER ASN LEU LYS THR ALA ASP THR SEQRES 8 H 217 ALA VAL TYR PHE CYS ALA ARG SER TRP TYR ASN ARG ALA SEQRES 9 H 217 MET ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SER SEQRES 10 H 217 SER ALA LYS THR THR ALA PRO SER VAL TYR PRO LEU ALA SEQRES 11 H 217 PRO VAL CYS GLY ASP THR THR GLY SER SER VAL THR LEU SEQRES 12 H 217 GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR SEQRES 13 H 217 LEU THR TRP ASN SER GLY SER LEU SER SER GLY VAL HIS SEQRES 14 H 217 THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SEQRES 15 H 217 SER SER SER VAL THR VAL THR SER SER THR TRP PRO SER SEQRES 16 H 217 GLN SER ILE THR CYS ASN VAL ALA HIS PRO ALA SER SER SEQRES 17 H 217 THR LYS VAL ASP LYS LYS ILE GLU PRO SEQRES 1 L 211 ASP ILE LEU MET THR GLN SER PRO SER SER LEU SER VAL SEQRES 2 L 211 SER VAL GLY SER SER VAL THR ILE THR CYS GLN ALA SER SEQRES 3 L 211 GLN ASN ILE THR ASN TYR ILE VAL TRP TYR GLN GLN LYS SEQRES 4 L 211 PRO GLY GLN ALA PRO LYS LEU LEU ILE TYR TYR THR SER SEQRES 5 L 211 THR LEU GLU SER GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 L 211 GLY SER GLY ARG ASP TYR SER PHE THR ILE SER ASN LEU SEQRES 7 L 211 GLN PRO GLU ASP VAL ALA THR TYR TYR CYS LEU GLN TYR SEQRES 8 L 211 ASN SER LEU LEU THR PHE GLY GLY GLY THR LYS LEU GLU SEQRES 9 L 211 ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE SEQRES 10 L 211 PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER SEQRES 11 L 211 VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASN ILE SEQRES 12 L 211 ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN SEQRES 13 L 211 GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SEQRES 14 L 211 SER THR TYR SER MET SER SER THR LEU THR LEU THR LYS SEQRES 15 L 211 ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA SEQRES 16 L 211 THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE SEQRES 17 L 211 ASN ARG ASN HET GYP A 501 13 HETNAM GYP METHYL ALPHA-D-GLUCOPYRANOSIDE HETSYN GYP METHYL-ALPHA-D-GLUCOPYRANOSIDE; ALPHA-METHYL-D- HETSYN 2 GYP GLUCOPYRANOSIDE; METHYL ALPHA-D-GLUCOSIDE; METHYL D- HETSYN 3 GYP GLUCOSIDE; METHYL GLUCOSIDE FORMUL 4 GYP C7 H14 O6 FORMUL 5 HOH *45(H2 O) HELIX 1 1 ASP A 22 ARG A 29 1 8 HELIX 2 2 ARG A 29 MET A 53 1 25 HELIX 3 3 LEU A 54 ALA A 57 5 4 HELIX 4 4 LEU A 62 GLY A 66 5 5 HELIX 5 5 THR A 70 LEU A 80 1 11 HELIX 6 6 LEU A 80 GLY A 100 1 21 HELIX 7 7 GLY A 100 ILE A 111 1 12 HELIX 8 8 LEU A 112 VAL A 123 1 12 HELIX 9 9 PRO A 129 GLY A 141 1 13 HELIX 10 10 PHE A 142 GLY A 144 5 3 HELIX 11 11 ALA A 145 PHE A 158 1 14 HELIX 12 12 LYS A 162 VAL A 189 1 28 HELIX 13 13 ALA A 213 ILE A 218 1 6 HELIX 14 14 TRP A 219 MET A 234 1 16 HELIX 15 15 TRP A 257 SER A 281 1 25 HELIX 16 16 PHE A 295 GLY A 316 1 22 HELIX 17 17 GLY A 316 LEU A 334 1 19 HELIX 18 18 LEU A 335 LEU A 339 5 5 HELIX 19 19 SER A 347 GLY A 389 1 43 HELIX 20 20 SER A 391 ALA A 415 1 25 HELIX 21 21 ILE A 416 THR A 432 1 17 HELIX 22 22 PRO A 435 TYR A 457 1 23 HELIX 23 23 SER H 28 TYR H 32 5 5 HELIX 24 24 ALA H 62 LYS H 65 5 4 HELIX 25 25 LYS H 87 THR H 91 5 5 HELIX 26 26 SER H 161 SER H 163 5 3 HELIX 27 27 PRO H 205 SER H 208 5 4 HELIX 28 28 GLN L 79 VAL L 83 5 5 HELIX 29 29 SER L 120 THR L 125 1 6 HELIX 30 30 LYS L 182 HIS L 188 1 7 SHEET 1 A 2 VAL A 14 ILE A 15 0 SHEET 2 A 2 ASP A 236 LEU A 237 1 O ASP A 236 N ILE A 15 SHEET 1 B 4 GLN H 3 GLN H 6 0 SHEET 2 B 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 B 4 THR H 78 LEU H 83 -1 O LEU H 83 N VAL H 18 SHEET 4 B 4 PHE H 68 ASP H 73 -1 N SER H 69 O GLN H 82 SHEET 1 C 6 GLY H 10 LYS H 12 0 SHEET 2 C 6 THR H 112 VAL H 116 1 O THR H 115 N LYS H 12 SHEET 3 C 6 ALA H 92 ARG H 98 -1 N ALA H 92 O VAL H 114 SHEET 4 C 6 MET H 34 GLN H 39 -1 N ASN H 35 O ALA H 97 SHEET 5 C 6 GLU H 46 ILE H 51 -1 O GLU H 46 N LYS H 38 SHEET 6 C 6 THR H 58 TYR H 60 -1 O THR H 59 N TRP H 50 SHEET 1 D 4 GLY H 10 LYS H 12 0 SHEET 2 D 4 THR H 112 VAL H 116 1 O THR H 115 N LYS H 12 SHEET 3 D 4 ALA H 92 ARG H 98 -1 N ALA H 92 O VAL H 114 SHEET 4 D 4 TYR H 107 TRP H 108 -1 O TYR H 107 N ARG H 98 SHEET 1 E 4 SER H 125 LEU H 129 0 SHEET 2 E 4 SER H 140 TYR H 150 -1 O LEU H 146 N TYR H 127 SHEET 3 E 4 LEU H 179 THR H 189 -1 O VAL H 188 N VAL H 141 SHEET 4 E 4 VAL H 168 GLN H 176 -1 N PHE H 171 O SER H 183 SHEET 1 F 3 THR H 156 TRP H 159 0 SHEET 2 F 3 THR H 199 HIS H 204 -1 O ALA H 203 N THR H 156 SHEET 3 F 3 THR H 209 LYS H 214 -1 O LYS H 213 N CYS H 200 SHEET 1 G 4 MET L 4 SER L 7 0 SHEET 2 G 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 G 4 ASP L 70 ILE L 75 -1 O PHE L 73 N ILE L 21 SHEET 4 G 4 PHE L 62 SER L 67 -1 N SER L 65 O SER L 72 SHEET 1 H 6 SER L 10 SER L 14 0 SHEET 2 H 6 THR L 101 LYS L 106 1 O GLU L 104 N LEU L 11 SHEET 3 H 6 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 103 SHEET 4 H 6 ILE L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 H 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 H 6 THR L 53 LEU L 54 -1 O THR L 53 N TYR L 49 SHEET 1 I 4 SER L 10 SER L 14 0 SHEET 2 I 4 THR L 101 LYS L 106 1 O GLU L 104 N LEU L 11 SHEET 3 I 4 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 103 SHEET 4 I 4 THR L 96 PHE L 97 -1 O THR L 96 N GLN L 90 SHEET 1 J 4 THR L 113 PHE L 117 0 SHEET 2 J 4 GLY L 128 PHE L 138 -1 O PHE L 134 N SER L 115 SHEET 3 J 4 TYR L 172 THR L 181 -1 O LEU L 180 N ALA L 129 SHEET 4 J 4 VAL L 158 TRP L 162 -1 N LEU L 159 O THR L 177 SHEET 1 K 4 SER L 152 ARG L 154 0 SHEET 2 K 4 ASN L 144 ILE L 149 -1 N ILE L 149 O SER L 152 SHEET 3 K 4 SER L 190 THR L 196 -1 O THR L 192 N LYS L 148 SHEET 4 K 4 ILE L 204 ASN L 209 -1 O ILE L 204 N ALA L 195 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.08 SSBOND 2 CYS H 145 CYS H 200 1555 1555 2.04 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.10 SSBOND 4 CYS L 133 CYS L 193 1555 1555 2.03 CISPEP 1 PHE H 151 PRO H 152 0 -7.92 CISPEP 2 GLU H 153 PRO H 154 0 0.44 CISPEP 3 TRP H 193 PRO H 194 0 0.87 CISPEP 4 SER L 7 PRO L 8 0 -5.76 CISPEP 5 TYR L 139 PRO L 140 0 3.55 CRYST1 138.266 86.545 144.789 90.00 115.41 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 0.007232 0.000000 0.003435 0.00000 SCALE2 0.000000 0.011555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007646 0.00000