HEADER OXIDOREDUCTASE 09-FEB-09 3G79 TITLE CRYSTAL STRUCTURE OF NDP-N-ACETYL-D-GALACTOSAMINURONIC ACID TITLE 2 DEHYDROGENASE FROM METHANOSARCINA MAZEI GO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NDP-N-ACETYL-D-GALACTOSAMINURONIC ACID DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 3-469; COMPND 5 EC: 1.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI GO1; SOURCE 3 ORGANISM_TAXID: 192952; SOURCE 4 STRAIN: GO1 / DSM 3647 / GOE1 / JCM 11883 / OCM 88; SOURCE 5 ATCC: BAA-159; SOURCE 6 GENE: MM_1154; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BC-PSGX3(BC) KEYWDS STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NEW YORK KEYWDS 2 STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, NDP-N-ACETYL-D- KEYWDS 3 GALACTOSAMINURONIC ACID DEHYDROGENASE, OXIDOREDUCTASE, PSI-2, NEW KEYWDS 4 YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR V.N.MALASHKEVICH,R.TORO,J.M.SAUDER,S.K.BURLEY,S.C.ALMO,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 21-FEB-24 3G79 1 REMARK REVDAT 5 10-FEB-21 3G79 1 AUTHOR JRNL SEQADV REVDAT 4 21-NOV-18 3G79 1 AUTHOR REVDAT 3 01-NOV-17 3G79 1 REMARK REVDAT 2 13-JUL-11 3G79 1 VERSN REVDAT 1 17-FEB-09 3G79 0 JRNL AUTH V.N.MALASHKEVICH,J.M.SAUDER,S.K.BURLEY,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF NDP-N-ACETYL-D-GALACTOSAMINURONIC ACID JRNL TITL 2 DEHYDROGENASE FROM METHANOSARCINA MAZEI GO1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 40272 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2038 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2843 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.516 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.324 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.251 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.706 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7406 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10010 ; 1.890 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 950 ; 7.335 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 306 ;37.859 ;24.183 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1300 ;21.884 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;20.946 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1120 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5542 ; 0.008 ; 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): 4710 ; 1.134 ; 3.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7556 ; 4.753 ;50.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2696 ;11.746 ;50.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2454 ; 1.043 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B -999 B 999 1 REMARK 3 1 A -999 A 999 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 3633 ; 0.820 ; 5.000 REMARK 3 TIGHT THERMAL 1 B (A**2): 3633 ; 3.410 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 478 REMARK 3 ORIGIN FOR THE GROUP (A): 10.0963 -5.1560 -2.8526 REMARK 3 T TENSOR REMARK 3 T11: 0.0242 T22: 0.0345 REMARK 3 T33: 0.1025 T12: -0.0159 REMARK 3 T13: -0.0160 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 0.2571 L22: 0.8596 REMARK 3 L33: 0.7693 L12: -0.0443 REMARK 3 L13: -0.1625 L23: 0.2430 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: 0.0689 S13: 0.0791 REMARK 3 S21: 0.0205 S22: -0.0247 S23: 0.0467 REMARK 3 S31: -0.1143 S32: 0.0481 S33: 0.0109 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 478 REMARK 3 ORIGIN FOR THE GROUP (A): 9.9315 -42.2439 -0.7879 REMARK 3 T TENSOR REMARK 3 T11: 0.0223 T22: 0.0243 REMARK 3 T33: 0.0879 T12: 0.0077 REMARK 3 T13: 0.0059 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.4720 L22: 0.5491 REMARK 3 L33: 0.7073 L12: 0.3527 REMARK 3 L13: 0.3132 L23: 0.3066 REMARK 3 S TENSOR REMARK 3 S11: 0.0344 S12: -0.0311 S13: -0.0828 REMARK 3 S21: 0.0586 S22: -0.0667 S23: -0.0011 REMARK 3 S31: 0.1169 S32: 0.0559 S33: 0.0323 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. 3. THE REMARK 3 FRIEDEL PAIRS WERE USED IN PHASING. REMARK 4 REMARK 4 3G79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86212 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 : 4.200 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.8080 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.21900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: RESOLVE 2.13, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3000, 0.1M CITRATE, PH 5.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 39.41500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.36150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.36150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 SER A 2 REMARK 465 LEU A 3 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 LEU B 3 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 GLU A 61 CG CD OE1 OE2 REMARK 470 GLU B 61 CG CD OE1 OE2 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 GLU A 74 N GLY A 76 1.88 REMARK 500 O ASN B 115 N LYS B 117 1.94 REMARK 500 O ALA A 342 CG GLU A 345 2.03 REMARK 500 OG SER A 53 O HOH A 609 2.19 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 PRO A 315 C - N - CA ANGL. DEV. = -9.4 DEGREES REMARK 500 PRO B 112 C - N - CA ANGL. DEV. = 12.7 DEGREES REMARK 500 LEU B 176 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG B 326 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 326 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET B 336 CG - SD - CE ANGL. DEV. = -12.8 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 LYS A 19 -31.72 -131.59 REMARK 500 CYS A 42 -37.46 98.28 REMARK 500 SER A 53 97.72 -65.47 REMARK 500 LYS A 54 120.23 -37.85 REMARK 500 SER A 55 -38.69 116.96 REMARK 500 SER A 68 -148.39 -110.19 REMARK 500 PRO A 69 -134.44 -112.78 REMARK 500 LYS A 71 6.67 110.63 REMARK 500 GLU A 74 53.56 30.34 REMARK 500 PRO A 75 49.40 -37.57 REMARK 500 THR A 111 57.39 -112.25 REMARK 500 ALA A 114 -165.55 86.68 REMARK 500 LYS A 117 159.50 83.01 REMARK 500 ASP A 118 167.88 51.18 REMARK 500 GLU A 172 -62.19 -128.22 REMARK 500 VAL A 220 -48.90 109.39 REMARK 500 MET A 226 -168.95 -161.49 REMARK 500 LEU A 283 -154.97 -82.23 REMARK 500 HIS A 292 -63.97 -95.54 REMARK 500 ALA A 318 -126.45 77.57 REMARK 500 ASP A 319 113.74 81.52 REMARK 500 LYS A 365 98.98 -44.80 REMARK 500 ASP A 366 32.84 78.72 REMARK 500 ASP A 393 127.47 -171.41 REMARK 500 ASN A 398 64.65 72.00 REMARK 500 HIS A 424 151.99 -45.75 REMARK 500 ALA A 440 178.77 54.51 REMARK 500 LYS A 441 -59.45 133.36 REMARK 500 ALA A 442 -66.52 106.32 REMARK 500 ASN A 443 77.52 -118.16 REMARK 500 GLU A 471 -125.95 5.69 REMARK 500 GLU B 44 -81.18 -87.93 REMARK 500 GLU B 74 91.01 30.00 REMARK 500 ILE B 99 -44.65 116.69 REMARK 500 ALA B 108 54.50 -117.28 REMARK 500 PHE B 113 120.79 90.56 REMARK 500 ALA B 114 -76.80 -67.11 REMARK 500 PRO B 116 40.79 -55.23 REMARK 500 LYS B 117 77.88 -60.25 REMARK 500 ASP B 118 -135.23 39.76 REMARK 500 GLU B 172 -65.97 -139.71 REMARK 500 LEU B 188 -71.57 -53.21 REMARK 500 VAL B 220 -34.12 118.42 REMARK 500 MET B 226 -169.64 -163.91 REMARK 500 ARG B 280 -34.52 85.74 REMARK 500 ARG B 309 36.84 36.70 REMARK 500 GLU B 316 -116.40 -157.97 REMARK 500 ALA B 318 -152.29 -65.33 REMARK 500 LYS B 350 -86.30 64.87 REMARK 500 MET B 351 -58.58 125.36 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. 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 PRO A 112 PHE A 113 -148.84 REMARK 500 GLY A 472 HIS A 473 148.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11151G RELATED DB: TARGETDB DBREF 3G79 A 4 470 UNP Q8PXR2 Q8PXR2_METMA 3 469 DBREF 3G79 B 4 470 UNP Q8PXR2 Q8PXR2_METMA 3 469 SEQADV 3G79 MET A 1 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 SER A 2 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 LEU A 3 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 GLU A 471 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 GLY A 472 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS A 473 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS A 474 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS A 475 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS A 476 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS A 477 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS A 478 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 MET B 1 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 SER B 2 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 LEU B 3 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 GLU B 471 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 GLY B 472 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS B 473 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS B 474 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS B 475 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS B 476 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS B 477 UNP Q8PXR2 EXPRESSION TAG SEQADV 3G79 HIS B 478 UNP Q8PXR2 EXPRESSION TAG SEQRES 1 A 478 MET SER LEU SER MET SER LYS LEU GLU LYS LEU LEU LYS SEQRES 2 A 478 GLU ARG GLY PRO ILE LYS LYS ILE GLY VAL LEU GLY MET SEQRES 3 A 478 GLY TYR VAL GLY ILE PRO ALA ALA VAL LEU PHE ALA ASP SEQRES 4 A 478 ALA PRO CYS PHE GLU LYS VAL LEU GLY PHE GLN ARG ASN SEQRES 5 A 478 SER LYS SER SER GLY TYR LYS ILE GLU MET LEU ASN ARG SEQRES 6 A 478 GLY GLU SER PRO LEU LYS GLY GLU GLU PRO GLY LEU GLU SEQRES 7 A 478 GLU LEU ILE GLY LYS VAL VAL LYS ALA GLY LYS PHE GLU SEQRES 8 A 478 CYS THR PRO ASP PHE SER ARG ILE SER GLU LEU ASP ALA SEQRES 9 A 478 VAL THR LEU ALA ILE GLN THR PRO PHE ALA ASN PRO LYS SEQRES 10 A 478 ASP LEU GLU PRO ASP PHE SER ALA LEU ILE ASP GLY ILE SEQRES 11 A 478 ARG ASN VAL GLY LYS TYR LEU LYS PRO GLY MET LEU VAL SEQRES 12 A 478 VAL LEU GLU SER THR ILE THR PRO GLY THR THR GLU GLY SEQRES 13 A 478 MET ALA LYS GLN ILE LEU GLU GLU GLU SER GLY LEU LYS SEQRES 14 A 478 ALA GLY GLU ASP PHE ALA LEU ALA HIS ALA PRO GLU ARG SEQRES 15 A 478 VAL MET VAL GLY ARG LEU LEU LYS ASN ILE ARG GLU HIS SEQRES 16 A 478 ASP ARG ILE VAL GLY GLY ILE ASP GLU ALA SER THR LYS SEQRES 17 A 478 ARG ALA VAL GLU LEU TYR SER PRO VAL LEU THR VAL GLY SEQRES 18 A 478 GLN VAL ILE PRO MET SER ALA THR ALA ALA GLU VAL THR SEQRES 19 A 478 LYS THR ALA GLU ASN THR PHE ARG ASP LEU GLN ILE ALA SEQRES 20 A 478 ALA ILE ASN GLN LEU ALA LEU TYR CYS GLU ALA MET GLY SEQRES 21 A 478 ILE ASN VAL TYR ASP VAL ARG THR GLY VAL ASP SER LEU SEQRES 22 A 478 LYS GLY GLU GLY ILE THR ARG ALA VAL LEU TRP PRO GLY SEQRES 23 A 478 ALA GLY VAL GLY GLY HIS CYS LEU THR LYS ASP THR TYR SEQRES 24 A 478 HIS LEU GLU ARG GLY VAL LYS ILE GLY ARG GLY GLU LEU SEQRES 25 A 478 ASP TYR PRO GLU GLY ALA ASP SER ILE TYR VAL LEU ALA SEQRES 26 A 478 ARG LYS VAL ASN ASP PHE MET PRO ALA HIS MET TYR ASN SEQRES 27 A 478 LEU THR VAL ALA ALA LEU GLU ARG LEU GLY LYS LYS MET SEQRES 28 A 478 ASP GLY SER LYS VAL ALA MET LEU GLY TRP ALA PHE ILE SEQRES 29 A 478 LYS ASP SER ASP ASP ALA ARG ASN THR PRO SER GLU PRO SEQRES 30 A 478 TYR ARG ASP LEU CYS LEU LYS ALA GLY ALA SER VAL MET SEQRES 31 A 478 VAL HIS ASP PRO TYR VAL VAL ASN TYR PRO GLY VAL GLU SEQRES 32 A 478 ILE SER ASP ASN LEU GLU GLU VAL VAL ARG ASN ALA ASP SEQRES 33 A 478 ALA ILE VAL VAL LEU ALA GLY HIS SER ALA TYR SER SER SEQRES 34 A 478 LEU LYS ALA ASP TRP ALA LYS LYS VAL SER ALA LYS ALA SEQRES 35 A 478 ASN PRO VAL ILE ILE ASP GLY ARG ASN VAL ILE GLU PRO SEQRES 36 A 478 ASP GLU PHE ILE GLY LYS GLY PHE VAL TYR LYS GLY ILE SEQRES 37 A 478 GLY ARG GLU GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 478 MET SER LEU SER MET SER LYS LEU GLU LYS LEU LEU LYS SEQRES 2 B 478 GLU ARG GLY PRO ILE LYS LYS ILE GLY VAL LEU GLY MET SEQRES 3 B 478 GLY TYR VAL GLY ILE PRO ALA ALA VAL LEU PHE ALA ASP SEQRES 4 B 478 ALA PRO CYS PHE GLU LYS VAL LEU GLY PHE GLN ARG ASN SEQRES 5 B 478 SER LYS SER SER GLY TYR LYS ILE GLU MET LEU ASN ARG SEQRES 6 B 478 GLY GLU SER PRO LEU LYS GLY GLU GLU PRO GLY LEU GLU SEQRES 7 B 478 GLU LEU ILE GLY LYS VAL VAL LYS ALA GLY LYS PHE GLU SEQRES 8 B 478 CYS THR PRO ASP PHE SER ARG ILE SER GLU LEU ASP ALA SEQRES 9 B 478 VAL THR LEU ALA ILE GLN THR PRO PHE ALA ASN PRO LYS SEQRES 10 B 478 ASP LEU GLU PRO ASP PHE SER ALA LEU ILE ASP GLY ILE SEQRES 11 B 478 ARG ASN VAL GLY LYS TYR LEU LYS PRO GLY MET LEU VAL SEQRES 12 B 478 VAL LEU GLU SER THR ILE THR PRO GLY THR THR GLU GLY SEQRES 13 B 478 MET ALA LYS GLN ILE LEU GLU GLU GLU SER GLY LEU LYS SEQRES 14 B 478 ALA GLY GLU ASP PHE ALA LEU ALA HIS ALA PRO GLU ARG SEQRES 15 B 478 VAL MET VAL GLY ARG LEU LEU LYS ASN ILE ARG GLU HIS SEQRES 16 B 478 ASP ARG ILE VAL GLY GLY ILE ASP GLU ALA SER THR LYS SEQRES 17 B 478 ARG ALA VAL GLU LEU TYR SER PRO VAL LEU THR VAL GLY SEQRES 18 B 478 GLN VAL ILE PRO MET SER ALA THR ALA ALA GLU VAL THR SEQRES 19 B 478 LYS THR ALA GLU ASN THR PHE ARG ASP LEU GLN ILE ALA SEQRES 20 B 478 ALA ILE ASN GLN LEU ALA LEU TYR CYS GLU ALA MET GLY SEQRES 21 B 478 ILE ASN VAL TYR ASP VAL ARG THR GLY VAL ASP SER LEU SEQRES 22 B 478 LYS GLY GLU GLY ILE THR ARG ALA VAL LEU TRP PRO GLY SEQRES 23 B 478 ALA GLY VAL GLY GLY HIS CYS LEU THR LYS ASP THR TYR SEQRES 24 B 478 HIS LEU GLU ARG GLY VAL LYS ILE GLY ARG GLY GLU LEU SEQRES 25 B 478 ASP TYR PRO GLU GLY ALA ASP SER ILE TYR VAL LEU ALA SEQRES 26 B 478 ARG LYS VAL ASN ASP PHE MET PRO ALA HIS MET TYR ASN SEQRES 27 B 478 LEU THR VAL ALA ALA LEU GLU ARG LEU GLY LYS LYS MET SEQRES 28 B 478 ASP GLY SER LYS VAL ALA MET LEU GLY TRP ALA PHE ILE SEQRES 29 B 478 LYS ASP SER ASP ASP ALA ARG ASN THR PRO SER GLU PRO SEQRES 30 B 478 TYR ARG ASP LEU CYS LEU LYS ALA GLY ALA SER VAL MET SEQRES 31 B 478 VAL HIS ASP PRO TYR VAL VAL ASN TYR PRO GLY VAL GLU SEQRES 32 B 478 ILE SER ASP ASN LEU GLU GLU VAL VAL ARG ASN ALA ASP SEQRES 33 B 478 ALA ILE VAL VAL LEU ALA GLY HIS SER ALA TYR SER SER SEQRES 34 B 478 LEU LYS ALA ASP TRP ALA LYS LYS VAL SER ALA LYS ALA SEQRES 35 B 478 ASN PRO VAL ILE ILE ASP GLY ARG ASN VAL ILE GLU PRO SEQRES 36 B 478 ASP GLU PHE ILE GLY LYS GLY PHE VAL TYR LYS GLY ILE SEQRES 37 B 478 GLY ARG GLU GLY HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *179(H2 O) HELIX 1 1 SER A 6 GLY A 16 1 11 HELIX 2 2 VAL A 29 ALA A 40 1 12 HELIX 3 3 TYR A 58 ASN A 64 1 7 HELIX 4 4 GLU A 73 PRO A 75 5 3 HELIX 5 5 GLY A 76 ALA A 87 1 12 HELIX 6 6 ASP A 95 LEU A 102 5 8 HELIX 7 7 PHE A 123 LEU A 137 1 15 HELIX 8 8 GLY A 156 GLY A 167 1 12 HELIX 9 9 ARG A 187 HIS A 195 1 9 HELIX 10 10 ASP A 203 SER A 215 1 13 HELIX 11 11 PRO A 216 LEU A 218 5 3 HELIX 12 12 ALA A 228 MET A 259 1 32 HELIX 13 13 ASN A 262 SER A 272 1 11 HELIX 14 14 HIS A 292 LYS A 306 1 15 HELIX 15 15 SER A 320 ARG A 346 1 27 HELIX 16 16 PRO A 374 GLY A 386 1 13 HELIX 17 17 ASN A 407 ARG A 413 1 7 HELIX 18 18 HIS A 424 SER A 429 1 6 HELIX 19 19 LYS A 431 ALA A 440 1 10 HELIX 20 20 GLU A 454 GLY A 460 1 7 HELIX 21 21 SER B 6 GLY B 16 1 11 HELIX 22 22 VAL B 29 ASP B 39 1 11 HELIX 23 23 GLY B 57 ASN B 64 1 8 HELIX 24 24 GLY B 76 ALA B 87 1 12 HELIX 25 25 PHE B 123 LEU B 137 1 15 HELIX 26 26 GLY B 156 GLY B 167 1 12 HELIX 27 27 ARG B 187 HIS B 195 1 9 HELIX 28 28 ASP B 203 SER B 215 1 13 HELIX 29 29 PRO B 216 LEU B 218 5 3 HELIX 30 30 ALA B 228 GLY B 260 1 33 HELIX 31 31 ASN B 262 SER B 272 1 11 HELIX 32 32 HIS B 292 GLY B 308 1 17 HELIX 33 33 SER B 320 ARG B 346 1 27 HELIX 34 34 PRO B 374 GLY B 386 1 13 HELIX 35 35 HIS B 424 SER B 428 5 5 HELIX 36 36 LYS B 431 ALA B 440 1 10 HELIX 37 37 GLU B 454 GLY B 460 1 7 SHEET 1 A 8 PHE A 90 THR A 93 0 SHEET 2 A 8 LYS A 45 PHE A 49 1 N GLY A 48 O THR A 93 SHEET 3 A 8 LYS A 20 LEU A 24 1 N VAL A 23 O LEU A 47 SHEET 4 A 8 ALA A 104 LEU A 107 1 O THR A 106 N LEU A 24 SHEET 5 A 8 LEU A 142 LEU A 145 1 O VAL A 144 N LEU A 107 SHEET 6 A 8 ALA A 175 HIS A 178 1 O ALA A 175 N VAL A 143 SHEET 7 A 8 ARG A 197 GLY A 201 -1 O GLY A 200 N HIS A 178 SHEET 8 A 8 VAL A 223 SER A 227 1 O ILE A 224 N ARG A 197 SHEET 1 B 6 ILE A 404 SER A 405 0 SHEET 2 B 6 SER A 388 HIS A 392 1 N VAL A 391 O SER A 405 SHEET 3 B 6 LYS A 355 LEU A 359 1 N MET A 358 O HIS A 392 SHEET 4 B 6 ALA A 417 VAL A 420 1 O VAL A 419 N LEU A 359 SHEET 5 B 6 VAL A 445 ASP A 448 1 O ILE A 447 N ILE A 418 SHEET 6 B 6 VAL A 464 GLY A 467 1 O LYS A 466 N ASP A 448 SHEET 1 C 8 PHE B 90 THR B 93 0 SHEET 2 C 8 LYS B 45 PHE B 49 1 N GLY B 48 O THR B 93 SHEET 3 C 8 LYS B 20 LEU B 24 1 N VAL B 23 O LEU B 47 SHEET 4 C 8 ALA B 104 LEU B 107 1 O THR B 106 N GLY B 22 SHEET 5 C 8 LEU B 142 LEU B 145 1 O LEU B 142 N VAL B 105 SHEET 6 C 8 ALA B 175 HIS B 178 1 O ALA B 177 N LEU B 145 SHEET 7 C 8 ARG B 197 GLY B 201 -1 O GLY B 200 N HIS B 178 SHEET 8 C 8 VAL B 223 SER B 227 1 O ILE B 224 N ARG B 197 SHEET 1 D 6 ILE B 404 SER B 405 0 SHEET 2 D 6 SER B 388 HIS B 392 1 N VAL B 391 O SER B 405 SHEET 3 D 6 LYS B 355 LEU B 359 1 N MET B 358 O HIS B 392 SHEET 4 D 6 ALA B 417 VAL B 420 1 O VAL B 419 N LEU B 359 SHEET 5 D 6 VAL B 445 ASP B 448 1 O ILE B 447 N VAL B 420 SHEET 6 D 6 VAL B 464 GLY B 467 1 O VAL B 464 N ILE B 446 CISPEP 1 PHE A 113 ALA A 114 0 -13.10 CISPEP 2 ALA A 114 ASN A 115 0 1.49 CISPEP 3 ASP A 118 LEU A 119 0 -17.74 CISPEP 4 GLY A 275 GLU A 276 0 11.19 CISPEP 5 GLU A 471 GLY A 472 0 2.84 CISPEP 6 LYS B 71 GLY B 72 0 -2.91 CISPEP 7 GLU B 471 GLY B 472 0 2.40 CRYST1 78.830 88.723 151.600 90.00 90.00 90.00 P 21 21 21 8 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 0.012686 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006596 0.00000