PDB Short entry for 5ZVX HEADER ISOMERASE 13-MAY-18 5ZVX TITLE CRYSTAL STRUCTURE OF K86A MUTANT OF PHOSPHOMANNOSE ISOMERASE FROM TITLE 2 SALMONELLA TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSE-6-PHOSPHATE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOHEXOMUTASE,PHOSPHOMANNOSE ISOMERASE,PMI; COMPND 5 EC: 5.3.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / SOURCE 3 ATCC 700720); SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: MANA, PMI, STM1467; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, ZINC BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BANGERA,M.R.N.MURTHY REVDAT 3 22-NOV-23 5ZVX 1 REMARK REVDAT 2 22-MAY-19 5ZVX 1 JRNL REVDAT 1 01-MAY-19 5ZVX 0 JRNL AUTH M.BANGERA,G.GOWDA K,S.R.SAGURTHI,M.R.N.MURTHY JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO PHOSPHOMANNOSE JRNL TITL 2 ISOMERASE: THE ROLE OF ZINC AND CATALYTIC RESIDUES. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 475 2019 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 31063150 JRNL DOI 10.1107/S2059798319004169 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41443 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2195 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2978 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2944 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : 0.90000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3105 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2971 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4230 ; 1.918 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6833 ; 0.907 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 6.634 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;36.384 ;24.923 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 489 ;11.842 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.709 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 481 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3591 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 687 ; 0.002 ; 0.020 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): 1600 ; 1.841 ; 1.713 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1599 ; 1.835 ; 1.712 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2004 ; 2.700 ; 2.559 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2005 ; 2.701 ; 2.560 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1505 ; 2.414 ; 1.902 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1505 ; 2.411 ; 1.902 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2219 ; 3.652 ; 2.756 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3731 ; 6.032 ;15.613 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3732 ; 6.033 ;15.615 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ZVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 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) : 0.55000 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: PHASER REMARK 200 STARTING MODEL: 3H1M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.2 M SODIUM CACODYLATE PH 6.8, 20% PEG 8000,5% DIOXANE, REMARK 280 MICROBATCH, 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 18.09500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.33000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.86500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.33000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.09500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.86500 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 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 ALA A 51 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 29 CG CD OE1 NE2 REMARK 470 ASN A 52 CG OD1 ND2 REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 GLU A 63 CD OE1 OE2 REMARK 470 LYS A 64 CD CE NZ REMARK 470 ARG A 103 CZ NH1 NH2 REMARK 470 LYS A 111 CE NZ REMARK 470 ASP A 120 CG OD1 OD2 REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 LYS A 127 CD CE NZ REMARK 470 GLU A 222 CG CD OE1 OE2 REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLU A 294 CG CD OE1 OE2 REMARK 470 LYS A 296 CD CE NZ REMARK 470 LEU A 330 CG CD1 CD2 REMARK 470 GLN A 331 CG CD OE1 NE2 REMARK 470 GLU A 356 CG CD OE1 OE2 REMARK 470 LYS A 362 CE NZ 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 ZN ZN A 401 O HOH A 503 1.48 REMARK 500 O TYR A 281 O HOH A 502 2.04 REMARK 500 O1 EDO A 407 O HOH A 503 2.05 REMARK 500 CB ALA A 90 O HOH A 778 2.10 REMARK 500 NH1 ARG A 59 O HOH A 505 2.12 REMARK 500 O HOH A 834 O HOH A 859 2.13 REMARK 500 O HOH A 713 O HOH A 859 2.19 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 O HOH A 953 O HOH A 962 1655 2.13 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 CYS A 89 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 327 CB - CG - OD2 ANGL. DEV. = -6.3 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 ASN A 10 53.06 -93.85 REMARK 500 ASN A 27 61.89 -154.02 REMARK 500 SER A 44 87.17 -173.14 REMARK 500 ASN A 65 55.68 -156.60 REMARK 500 ALA A 114 18.52 -66.61 REMARK 500 ASP A 120 42.55 -77.08 REMARK 500 ALA A 147 159.45 73.64 REMARK 500 ASP A 355 -114.39 57.32 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 964 DISTANCE = 6.31 ANGSTROMS 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 NE2 REMARK 620 2 GLU A 134 OE1 101.4 REMARK 620 3 HIS A 255 NE2 107.6 103.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H1M RELATED DB: PDB REMARK 900 NATIVE PROTEIN REMARK 900 RELATED ID: 2WFP RELATED DB: PDB REMARK 900 NATIVE APO PROTEIN DBREF 5ZVX A 1 391 UNP P25081 MANA_SALTY 1 391 SEQADV 5ZVX ALA A -1 UNP P25081 EXPRESSION TAG SEQADV 5ZVX SER A 0 UNP P25081 EXPRESSION TAG SEQADV 5ZVX ALA A 86 UNP P25081 LYS 86 ENGINEERED MUTATION SEQRES 1 A 393 ALA SER MET GLN LYS LEU ILE ASN SER VAL GLN ASN TYR SEQRES 2 A 393 ALA TRP GLY SER LYS THR ALA LEU THR GLU LEU TYR GLY SEQRES 3 A 393 ILE ALA ASN PRO GLN GLN GLN PRO MET ALA GLU LEU TRP SEQRES 4 A 393 MET GLY ALA HIS PRO LYS SER SER SER ARG ILE THR THR SEQRES 5 A 393 ALA ASN GLY GLU THR VAL SER LEU ARG ASP ALA ILE GLU SEQRES 6 A 393 LYS ASN LYS THR ALA MET LEU GLY GLU ALA VAL ALA ASN SEQRES 7 A 393 ARG PHE GLY GLU LEU PRO PHE LEU PHE ALA VAL LEU CYS SEQRES 8 A 393 ALA ALA GLN PRO LEU SER ILE GLN VAL HIS PRO ASN LYS SEQRES 9 A 393 ARG ASN SER GLU ILE GLY PHE ALA LYS GLU ASN ALA ALA SEQRES 10 A 393 GLY ILE PRO MET ASP ALA ALA GLU ARG ASN TYR LYS ASP SEQRES 11 A 393 PRO ASN HIS LYS PRO GLU LEU VAL PHE ALA LEU THR PRO SEQRES 12 A 393 PHE LEU ALA MET ASN ALA PHE ARG GLU PHE SER ASP ILE SEQRES 13 A 393 VAL SER LEU LEU GLN PRO VAL ALA GLY ALA HIS SER ALA SEQRES 14 A 393 ILE ALA HIS PHE LEU GLN VAL PRO ASN ALA GLU ARG LEU SEQRES 15 A 393 SER GLN LEU PHE ALA SER LEU LEU ASN MET GLN GLY GLU SEQRES 16 A 393 GLU LYS SER ARG ALA LEU ALA VAL LEU LYS ALA ALA LEU SEQRES 17 A 393 ASN SER GLN GLN GLY GLU PRO TRP GLN THR ILE ARG VAL SEQRES 18 A 393 ILE SER GLU TYR TYR PRO ASP ASP SER GLY LEU PHE SER SEQRES 19 A 393 PRO LEU LEU LEU ASN VAL VAL LYS LEU ASN PRO GLY GLU SEQRES 20 A 393 ALA MET PHE LEU PHE ALA GLU THR PRO HIS ALA TYR LEU SEQRES 21 A 393 GLN GLY VAL ALA LEU GLU VAL MET ALA ASN SER ASP ASN SEQRES 22 A 393 VAL LEU ARG ALA GLY LEU THR PRO LYS TYR ILE ASP ILE SEQRES 23 A 393 PRO GLU LEU VAL ALA ASN VAL LYS PHE GLU PRO LYS PRO SEQRES 24 A 393 ALA GLY GLU LEU LEU THR ALA PRO VAL LYS SER GLY ALA SEQRES 25 A 393 GLU LEU ASP PHE PRO ILE PRO VAL ASP ASP PHE ALA PHE SEQRES 26 A 393 SER LEU HIS ASP LEU ALA LEU GLN GLU THR SER ILE GLY SEQRES 27 A 393 GLN HIS SER ALA ALA ILE LEU PHE CYS VAL GLU GLY GLU SEQRES 28 A 393 ALA VAL LEU ARG LYS ASP GLU GLN ARG LEU VAL LEU LYS SEQRES 29 A 393 PRO GLY GLU SER ALA PHE ILE GLY ALA ASP GLU SER PRO SEQRES 30 A 393 VAL ASN ALA SER GLY THR GLY ARG LEU ALA ARG VAL TYR SEQRES 31 A 393 ASN LYS LEU HET ZN A 401 1 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 EDO 6(C2 H6 O2) FORMUL 9 HOH *464(H2 O) HELIX 1 AA1 THR A 17 GLY A 24 1 8 HELIX 2 AA2 LEU A 58 ASN A 65 1 8 HELIX 3 AA3 ASN A 65 GLY A 71 1 7 HELIX 4 AA4 GLY A 71 GLY A 79 1 9 HELIX 5 AA5 ASN A 101 ALA A 114 1 14 HELIX 6 AA6 GLU A 150 GLN A 159 1 10 HELIX 7 AA7 PRO A 160 ALA A 164 5 5 HELIX 8 AA8 HIS A 165 VAL A 174 1 10 HELIX 9 AA9 ASN A 176 ASN A 189 1 14 HELIX 10 AB1 GLN A 191 GLN A 209 1 19 HELIX 11 AB2 PRO A 213 GLU A 222 1 10 HELIX 12 AB3 ASP A 227 LEU A 230 5 4 HELIX 13 AB4 PHE A 231 LEU A 235 1 5 HELIX 14 AB5 ASP A 283 ASN A 290 1 8 HELIX 15 AB6 PRO A 297 LEU A 301 5 5 HELIX 16 AB7 ALA A 371 SER A 374 5 4 SHEET 1 AA1 5 MET A 1 LYS A 3 0 SHEET 2 AA1 5 SER A 366 ILE A 369 -1 O PHE A 368 N GLN A 2 SHEET 3 AA1 5 ALA A 341 LYS A 354 -1 N ALA A 341 O ILE A 369 SHEET 4 AA1 5 VAL A 376 TYR A 388 -1 O SER A 379 N VAL A 351 SHEET 5 AA1 5 THR A 333 ILE A 335 -1 N THR A 333 O ALA A 378 SHEET 1 AA2 6 VAL A 306 SER A 308 0 SHEET 2 AA2 6 GLU A 311 PHE A 314 -1 O GLU A 311 N SER A 308 SHEET 3 AA2 6 ALA A 322 ASP A 327 -1 O LEU A 325 N LEU A 312 SHEET 4 AA2 6 VAL A 376 TYR A 388 -1 O ARG A 386 N SER A 324 SHEET 5 AA2 6 ALA A 341 LYS A 354 -1 N VAL A 351 O SER A 379 SHEET 6 AA2 6 GLN A 357 LEU A 361 -1 O LEU A 359 N LEU A 352 SHEET 1 AA3 6 SER A 7 GLN A 9 0 SHEET 2 AA3 6 GLU A 35 MET A 38 -1 O TRP A 37 N SER A 7 SHEET 3 AA3 6 PHE A 83 ALA A 90 -1 O PHE A 85 N MET A 38 SHEET 4 AA3 6 HIS A 255 ALA A 267 -1 O ALA A 262 N LEU A 88 SHEET 5 AA3 6 PHE A 142 PHE A 148 -1 N LEU A 143 O LEU A 258 SHEET 6 AA3 6 LEU A 236 LEU A 241 -1 O LEU A 241 N PHE A 142 SHEET 1 AA4 6 SER A 7 GLN A 9 0 SHEET 2 AA4 6 GLU A 35 MET A 38 -1 O TRP A 37 N SER A 7 SHEET 3 AA4 6 PHE A 83 ALA A 90 -1 O PHE A 85 N MET A 38 SHEET 4 AA4 6 HIS A 255 ALA A 267 -1 O ALA A 262 N LEU A 88 SHEET 5 AA4 6 GLU A 134 ALA A 138 -1 N PHE A 137 O LEU A 263 SHEET 6 AA4 6 ALA A 246 LEU A 249 -1 O LEU A 249 N GLU A 134 SHEET 1 AA5 2 ARG A 47 THR A 49 0 SHEET 2 AA5 2 THR A 55 SER A 57 -1 O VAL A 56 N ILE A 48 SHEET 1 AA6 2 GLN A 97 VAL A 98 0 SHEET 2 AA6 2 LEU A 273 ARG A 274 -1 O LEU A 273 N VAL A 98 LINK NE2 HIS A 99 ZN ZN A 401 1555 1555 2.21 LINK OE1 GLU A 134 ZN ZN A 401 1555 1555 1.98 LINK NE2 HIS A 255 ZN ZN A 401 1555 1555 2.12 CISPEP 1 GLU A 212 PRO A 213 0 1.90 CISPEP 2 SER A 374 PRO A 375 0 -3.47 SITE 1 AC1 5 HIS A 99 GLU A 134 HIS A 255 EDO A 407 SITE 2 AC1 5 HOH A 503 SITE 1 AC2 6 PHE A 137 ALA A 138 PRO A 243 GLY A 244 SITE 2 AC2 6 GLU A 347 ARG A 383 SITE 1 AC3 8 ASN A 10 ALA A 12 GLN A 31 PRO A 32 SITE 2 AC3 8 ALA A 304 HOH A 580 HOH A 599 HOH A 653 SITE 1 AC4 2 TRP A 13 HOH A 772 SITE 1 AC5 6 HIS A 131 VAL A 318 ASP A 319 ASP A 320 SITE 2 AC5 6 HOH A 508 HOH A 633 SITE 1 AC6 7 TYR A 224 PRO A 279 HOH A 558 HOH A 601 SITE 2 AC6 7 HOH A 645 HOH A 709 HOH A 751 SITE 1 AC7 9 LEU A 94 SER A 95 GLN A 97 HIS A 255 SITE 2 AC7 9 ALA A 256 TYR A 257 ZN A 401 HOH A 503 SITE 3 AC7 9 HOH A 669 CRYST1 36.190 91.730 116.660 90.00 90.00 90.00 P 21 21 21 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 0.027632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008572 0.00000