HEADER METAL BINDING PROTEIN 31-JAN-14 4OOA TITLE CRYSTAL STRUCTURE OF NAF1 (MINER1): H114C THE REDOX-ACTIVE 2FE-2S TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CDGSH IRON-SULFUR DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: ENDOPLASMIC RETICULUM INTERMEMBRANE SMALL PROTEIN, MITONEET- COMPND 5 RELATED 1 PROTEIN, MINER1, NUTRIENT-DEPRIVATION AUTOPHAGY FACTOR-1, COMPND 6 NAF-1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CISD2, CDGSH2, ERIS, ZCD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE BOUND, THIAZOLIDINEDIONE, OXIDATIVE STRESS, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.TAMIR,Y.EISENBERG-DOMOVICH,A.R.CONLAN,J.T.STOFLETH,C.H.LIPPER, AUTHOR 2 M.L.PADDOCK,R.MITTLER,P.A.JENNINGS,O.LIVNAH,R.NECHUSHTAI REVDAT 2 28-FEB-24 4OOA 1 REMARK SEQADV LINK REVDAT 1 02-JUL-14 4OOA 0 JRNL AUTH S.TAMIR,Y.EISENBERG-DOMOVICH,A.R.CONLAN,J.T.STOFLETH, JRNL AUTH 2 C.H.LIPPER,M.L.PADDOCK,R.MITTLER,P.A.JENNINGS,O.LIVNAH, JRNL AUTH 3 R.NECHUSHTAI JRNL TITL A POINT MUTATION IN THE [2FE-2S] CLUSTER BINDING REGION OF JRNL TITL 2 THE NAF-1 PROTEIN (H114C) DRAMATICALLY HINDERS THE CLUSTER JRNL TITL 3 DONOR PROPERTIES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 1572 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24914968 JRNL DOI 10.1107/S1399004714005458 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 50138 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2689 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2716 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3070 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : 0.28000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.159 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3125 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3051 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4188 ; 1.890 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7022 ; 0.768 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 390 ; 5.966 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;31.761 ;26.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 584 ;13.019 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ; 6.093 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3444 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 628 ; 0.001 ; 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): 1566 ; 1.993 ; 1.803 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1565 ; 1.977 ; 1.800 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1948 ; 2.489 ; 2.694 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1949 ; 2.108 ; 2.973 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1559 ; 2.240 ; 2.030 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1532 ; 2.042 ; 2.228 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2219 ; 2.060 ; 3.222 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3576 ; 2.694 ;16.154 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3481 ; 2.491 ;15.798 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6176 ; 2.966 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 73 ;22.833 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6296 ; 7.030 ; 5.000 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4OOA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 0.98 REMARK 200 MONOCHROMATOR : OPTICAL HUTCH REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54202 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 3500, 100 MM TRIS-HCL PH 8.0 REMARK 280 AND 100-200 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 24.19650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.62050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.49250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.62050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.19650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.49250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 4090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 3 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 GLU A 134 REMARK 465 VAL A 135 REMARK 465 ASP B 68 REMARK 465 VAL B 135 REMARK 465 ASP C 68 REMARK 465 LYS C 133 REMARK 465 GLU C 134 REMARK 465 VAL C 135 REMARK 465 ASP D 68 REMARK 465 LYS D 133 REMARK 465 GLU D 134 REMARK 465 VAL D 135 REMARK 465 ASP E 68 REMARK 465 GLU E 134 REMARK 465 VAL E 135 REMARK 465 VAL F 135 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 132 CD CE NZ REMARK 480 LYS A 133 CD CE NZ REMARK 480 LYS B 133 CD CE NZ REMARK 480 LYS C 116 CE NZ REMARK 480 GLU C 119 OE1 OE2 REMARK 480 LYS C 131 CE NZ REMARK 480 LYS C 132 CG CD CE NZ REMARK 480 LYS D 74 CD CE NZ REMARK 480 LYS D 95 CG CD CE NZ REMARK 480 LYS D 116 CD CE NZ REMARK 480 LYS D 131 NZ REMARK 480 LYS E 95 CE NZ REMARK 480 LYS E 116 CD CE NZ REMARK 480 LEU E 120 CG CD1 CD2 REMARK 480 LYS E 131 NZ REMARK 480 LYS E 133 CE NZ REMARK 480 ASP F 68 CB CG OD1 OD2 REMARK 480 LYS F 133 CD CE NZ REMARK 480 GLU F 134 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 OE2 GLU B 78 OH TYR C 98 2.17 REMARK 500 OH TYR C 98 O HOH C 334 2.18 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 GLU C 119 CD GLU C 119 OE1 -0.071 REMARK 500 ARG E 100 C CYS E 101 N 0.259 REMARK 500 ARG F 100 C CYS F 101 N 0.300 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 E 99 CA - CB - SG ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP F 68 N - CA - CB ANGL. DEV. = -17.1 DEGREES REMARK 500 GLU F 134 CB - CG - CD ANGL. DEV. = 16.5 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 124 39.64 -140.31 REMARK 500 ASN B 124 36.80 -143.14 REMARK 500 ASN E 124 39.69 -140.33 REMARK 500 ASN F 124 35.37 -140.82 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 FES A 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 FES A 200 S1 112.1 REMARK 620 3 FES A 200 S2 115.5 105.5 REMARK 620 4 CYS A 101 SG 103.0 105.8 114.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 110 SG REMARK 620 2 FES A 200 S1 107.6 REMARK 620 3 FES A 200 S2 121.8 104.1 REMARK 620 4 CYS A 114 SG 105.8 113.3 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 99 SG REMARK 620 2 FES B 200 S1 112.0 REMARK 620 3 FES B 200 S2 115.3 104.9 REMARK 620 4 CYS B 101 SG 100.7 108.3 115.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 110 SG REMARK 620 2 FES B 200 S1 107.2 REMARK 620 3 FES B 200 S2 120.8 103.7 REMARK 620 4 CYS B 114 SG 107.4 113.1 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES C 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 99 SG REMARK 620 2 FES C 200 S1 110.6 REMARK 620 3 FES C 200 S2 117.3 104.2 REMARK 620 4 CYS C 101 SG 101.5 109.7 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES C 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 110 SG REMARK 620 2 FES C 200 S1 106.3 REMARK 620 3 FES C 200 S2 121.3 103.5 REMARK 620 4 CYS C 114 SG 107.8 114.9 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES D 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 99 SG REMARK 620 2 FES D 200 S1 112.7 REMARK 620 3 FES D 200 S2 116.5 103.2 REMARK 620 4 CYS D 101 SG 101.4 108.9 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES D 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 110 SG REMARK 620 2 FES D 200 S1 106.0 REMARK 620 3 FES D 200 S2 121.8 103.6 REMARK 620 4 CYS D 114 SG 107.4 113.6 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES E 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 99 SG REMARK 620 2 FES E 200 S1 112.1 REMARK 620 3 FES E 200 S2 122.3 105.4 REMARK 620 4 CYS E 101 SG 95.6 109.1 111.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES E 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 110 SG REMARK 620 2 FES E 200 S1 106.8 REMARK 620 3 FES E 200 S2 121.7 103.8 REMARK 620 4 CYS E 114 SG 106.1 114.1 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES F 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 99 SG REMARK 620 2 FES F 200 S1 112.5 REMARK 620 3 FES F 200 S2 115.5 105.4 REMARK 620 4 CYS F 101 SG 102.4 108.1 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES F 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 110 SG REMARK 620 2 FES F 200 S1 106.5 REMARK 620 3 FES F 200 S2 123.2 104.5 REMARK 620 4 CYS F 114 SG 104.5 114.1 104.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES D 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES E 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES F 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OO7 RELATED DB: PDB REMARK 900 WILD TYPE (1.55 A) DBREF 4OOA A 68 135 UNP Q8N5K1 CISD2_HUMAN 68 135 DBREF 4OOA B 68 135 UNP Q8N5K1 CISD2_HUMAN 68 135 DBREF 4OOA C 68 135 UNP Q8N5K1 CISD2_HUMAN 68 135 DBREF 4OOA D 68 135 UNP Q8N5K1 CISD2_HUMAN 68 135 DBREF 4OOA E 68 135 UNP Q8N5K1 CISD2_HUMAN 68 135 DBREF 4OOA F 68 135 UNP Q8N5K1 CISD2_HUMAN 68 135 SEQADV 4OOA SER A 92 UNP Q8N5K1 CYS 92 ENGINEERED MUTATION SEQADV 4OOA CYS A 114 UNP Q8N5K1 HIS 114 ENGINEERED MUTATION SEQADV 4OOA SER B 92 UNP Q8N5K1 CYS 92 ENGINEERED MUTATION SEQADV 4OOA CYS B 114 UNP Q8N5K1 HIS 114 ENGINEERED MUTATION SEQADV 4OOA SER C 92 UNP Q8N5K1 CYS 92 ENGINEERED MUTATION SEQADV 4OOA CYS C 114 UNP Q8N5K1 HIS 114 ENGINEERED MUTATION SEQADV 4OOA SER D 92 UNP Q8N5K1 CYS 92 ENGINEERED MUTATION SEQADV 4OOA CYS D 114 UNP Q8N5K1 HIS 114 ENGINEERED MUTATION SEQADV 4OOA SER E 92 UNP Q8N5K1 CYS 92 ENGINEERED MUTATION SEQADV 4OOA CYS E 114 UNP Q8N5K1 HIS 114 ENGINEERED MUTATION SEQADV 4OOA SER F 92 UNP Q8N5K1 CYS 92 ENGINEERED MUTATION SEQADV 4OOA CYS F 114 UNP Q8N5K1 HIS 114 ENGINEERED MUTATION SEQRES 1 A 68 ASP SER LEU ILE ASN LEU LYS ILE GLN LYS GLU ASN PRO SEQRES 2 A 68 LYS VAL VAL ASN GLU ILE ASN ILE GLU ASP LEU SER LEU SEQRES 3 A 68 THR LYS ALA ALA TYR CYS ARG CYS TRP ARG SER LYS THR SEQRES 4 A 68 PHE PRO ALA CYS ASP GLY SER CYS ASN LYS HIS ASN GLU SEQRES 5 A 68 LEU THR GLY ASP ASN VAL GLY PRO LEU ILE LEU LYS LYS SEQRES 6 A 68 LYS GLU VAL SEQRES 1 B 68 ASP SER LEU ILE ASN LEU LYS ILE GLN LYS GLU ASN PRO SEQRES 2 B 68 LYS VAL VAL ASN GLU ILE ASN ILE GLU ASP LEU SER LEU SEQRES 3 B 68 THR LYS ALA ALA TYR CYS ARG CYS TRP ARG SER LYS THR SEQRES 4 B 68 PHE PRO ALA CYS ASP GLY SER CYS ASN LYS HIS ASN GLU SEQRES 5 B 68 LEU THR GLY ASP ASN VAL GLY PRO LEU ILE LEU LYS LYS SEQRES 6 B 68 LYS GLU VAL SEQRES 1 C 68 ASP SER LEU ILE ASN LEU LYS ILE GLN LYS GLU ASN PRO SEQRES 2 C 68 LYS VAL VAL ASN GLU ILE ASN ILE GLU ASP LEU SER LEU SEQRES 3 C 68 THR LYS ALA ALA TYR CYS ARG CYS TRP ARG SER LYS THR SEQRES 4 C 68 PHE PRO ALA CYS ASP GLY SER CYS ASN LYS HIS ASN GLU SEQRES 5 C 68 LEU THR GLY ASP ASN VAL GLY PRO LEU ILE LEU LYS LYS SEQRES 6 C 68 LYS GLU VAL SEQRES 1 D 68 ASP SER LEU ILE ASN LEU LYS ILE GLN LYS GLU ASN PRO SEQRES 2 D 68 LYS VAL VAL ASN GLU ILE ASN ILE GLU ASP LEU SER LEU SEQRES 3 D 68 THR LYS ALA ALA TYR CYS ARG CYS TRP ARG SER LYS THR SEQRES 4 D 68 PHE PRO ALA CYS ASP GLY SER CYS ASN LYS HIS ASN GLU SEQRES 5 D 68 LEU THR GLY ASP ASN VAL GLY PRO LEU ILE LEU LYS LYS SEQRES 6 D 68 LYS GLU VAL SEQRES 1 E 68 ASP SER LEU ILE ASN LEU LYS ILE GLN LYS GLU ASN PRO SEQRES 2 E 68 LYS VAL VAL ASN GLU ILE ASN ILE GLU ASP LEU SER LEU SEQRES 3 E 68 THR LYS ALA ALA TYR CYS ARG CYS TRP ARG SER LYS THR SEQRES 4 E 68 PHE PRO ALA CYS ASP GLY SER CYS ASN LYS HIS ASN GLU SEQRES 5 E 68 LEU THR GLY ASP ASN VAL GLY PRO LEU ILE LEU LYS LYS SEQRES 6 E 68 LYS GLU VAL SEQRES 1 F 68 ASP SER LEU ILE ASN LEU LYS ILE GLN LYS GLU ASN PRO SEQRES 2 F 68 LYS VAL VAL ASN GLU ILE ASN ILE GLU ASP LEU SER LEU SEQRES 3 F 68 THR LYS ALA ALA TYR CYS ARG CYS TRP ARG SER LYS THR SEQRES 4 F 68 PHE PRO ALA CYS ASP GLY SER CYS ASN LYS HIS ASN GLU SEQRES 5 F 68 LEU THR GLY ASP ASN VAL GLY PRO LEU ILE LEU LYS LYS SEQRES 6 F 68 LYS GLU VAL HET FES A 200 4 HET FES B 200 4 HET FES C 200 4 HET FES D 200 4 HET FES E 200 4 HET FES F 200 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 7 FES 6(FE2 S2) FORMUL 13 HOH *264(H2 O) HELIX 1 1 GLU A 89 LEU A 91 5 3 HELIX 2 2 GLY A 112 GLY A 122 1 11 HELIX 3 3 GLU B 89 LEU B 91 5 3 HELIX 4 4 GLY B 112 GLY B 122 1 11 HELIX 5 5 GLU C 89 LEU C 91 5 3 HELIX 6 6 GLY C 112 GLY C 122 1 11 HELIX 7 7 GLU D 89 LEU D 91 5 3 HELIX 8 8 GLY D 112 GLY D 122 1 11 HELIX 9 9 GLU E 89 LEU E 91 5 3 HELIX 10 10 GLY E 112 GLY E 122 1 11 HELIX 11 11 GLU F 89 LEU F 91 5 3 HELIX 12 12 GLY F 112 GLY F 122 1 11 SHEET 1 A 3 VAL A 82 ASN A 87 0 SHEET 2 A 3 VAL B 125 LYS B 131 1 O LYS B 131 N ILE A 86 SHEET 3 A 3 LYS B 95 TYR B 98 -1 N TYR B 98 O LEU B 128 SHEET 1 B 3 LYS A 95 TYR A 98 0 SHEET 2 B 3 LEU A 128 LYS A 131 -1 O LEU A 128 N TYR A 98 SHEET 3 B 3 ASN B 84 ASN B 87 1 O ILE B 86 N ILE A 129 SHEET 1 C 3 VAL C 82 ASN C 87 0 SHEET 2 C 3 VAL D 125 LYS D 131 1 O LYS D 131 N ILE C 86 SHEET 3 C 3 LYS D 95 TYR D 98 -1 N ALA D 96 O LEU D 130 SHEET 1 D 3 LYS C 95 TYR C 98 0 SHEET 2 D 3 VAL C 125 LYS C 131 -1 O LEU C 130 N ALA C 96 SHEET 3 D 3 VAL D 82 ASN D 87 1 O ASN D 84 N ILE C 129 SHEET 1 E 3 ASN E 84 ASN E 87 0 SHEET 2 E 3 LEU F 128 LYS F 131 1 O LYS F 131 N ILE E 86 SHEET 3 E 3 LYS F 95 TYR F 98 -1 N ALA F 96 O LEU F 130 SHEET 1 F 3 LYS E 95 TYR E 98 0 SHEET 2 F 3 LEU E 128 LYS E 131 -1 O LEU E 130 N ALA E 96 SHEET 3 F 3 ASN F 84 ASN F 87 1 O ASN F 84 N ILE E 129 LINK SG CYS A 99 FE1 FES A 200 1555 1555 2.29 LINK SG CYS A 101 FE1 FES A 200 1555 1555 2.11 LINK SG CYS A 110 FE2 FES A 200 1555 1555 2.27 LINK SG CYS A 114 FE2 FES A 200 1555 1555 2.34 LINK SG CYS B 99 FE1 FES B 200 1555 1555 2.26 LINK SG CYS B 101 FE1 FES B 200 1555 1555 2.23 LINK SG CYS B 110 FE2 FES B 200 1555 1555 2.28 LINK SG CYS B 114 FE2 FES B 200 1555 1555 2.33 LINK SG CYS C 99 FE1 FES C 200 1555 1555 2.19 LINK SG CYS C 101 FE1 FES C 200 1555 1555 2.08 LINK SG CYS C 110 FE2 FES C 200 1555 1555 2.27 LINK SG CYS C 114 FE2 FES C 200 1555 1555 2.32 LINK SG CYS D 99 FE1 FES D 200 1555 1555 2.19 LINK SG CYS D 101 FE1 FES D 200 1555 1555 2.15 LINK SG CYS D 110 FE2 FES D 200 1555 1555 2.30 LINK SG CYS D 114 FE2 FES D 200 1555 1555 2.32 LINK SG CYS E 99 FE1 FES E 200 1555 1555 2.18 LINK SG CYS E 101 FE1 FES E 200 1555 1555 2.11 LINK SG CYS E 110 FE2 FES E 200 1555 1555 2.28 LINK SG CYS E 114 FE2 FES E 200 1555 1555 2.32 LINK SG CYS F 99 FE1 FES F 200 1555 1555 2.25 LINK SG CYS F 101 FE1 FES F 200 1555 1555 2.12 LINK SG CYS F 110 FE2 FES F 200 1555 1555 2.26 LINK SG CYS F 114 FE2 FES F 200 1555 1555 2.34 CISPEP 1 PHE A 107 PRO A 108 0 11.07 CISPEP 2 PHE B 107 PRO B 108 0 12.65 CISPEP 3 PHE C 107 PRO C 108 0 8.60 CISPEP 4 PHE D 107 PRO D 108 0 11.08 CISPEP 5 PHE E 107 PRO E 108 0 10.10 CISPEP 6 PHE F 107 PRO F 108 0 12.75 SITE 1 AC1 9 CYS A 99 ARG A 100 CYS A 101 CYS A 110 SITE 2 AC1 9 ASP A 111 GLY A 112 SER A 113 CYS A 114 SITE 3 AC1 9 PRO A 127 SITE 1 AC2 10 CYS B 99 ARG B 100 CYS B 101 SER B 104 SITE 2 AC2 10 CYS B 110 ASP B 111 GLY B 112 SER B 113 SITE 3 AC2 10 CYS B 114 PRO B 127 SITE 1 AC3 10 CYS C 99 ARG C 100 CYS C 101 SER C 104 SITE 2 AC3 10 CYS C 110 ASP C 111 GLY C 112 SER C 113 SITE 3 AC3 10 CYS C 114 PRO C 127 SITE 1 AC4 8 CYS D 99 ARG D 100 CYS D 101 SER D 104 SITE 2 AC4 8 CYS D 110 ASP D 111 SER D 113 CYS D 114 SITE 1 AC5 9 CYS E 99 ARG E 100 CYS E 101 SER E 104 SITE 2 AC5 9 CYS E 110 ASP E 111 GLY E 112 SER E 113 SITE 3 AC5 9 CYS E 114 SITE 1 AC6 8 CYS F 99 ARG F 100 CYS F 101 CYS F 110 SITE 2 AC6 8 ASP F 111 SER F 113 CYS F 114 PRO F 127 CRYST1 48.393 60.985 135.241 90.00 90.00 90.00 P 21 21 21 24 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 0.020664 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016397 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007394 0.00000